Update
 

Checked for vaccum leaks and found a hole on the underside of the right rubber sleeve connecting the plenum to the right hand side intake manifold (as seen from behind the car) Will fit a new one ASAP. It was quite a big hole too. Can this explain the codes on the bank 1 cylinders?

yes, it can. Once you fix that, check for more leaks. I would grab a vacuum gauge from HF (they are cheap) and then see what you are getting with the car running. You can also use one of those handheld mini vacuum pumps that some use for doing brake bleeding. You should be able to hold vacuum if there are no leaks. Just T it into the line off the check valve.

One thing a smoke test wont tell you always is if the reservoir is cracked. They can crack on the underside which only shows up when there is vacuum.

How are you going to hold vacuum with a handheld mini vacuum pump on the intake system?

Your going to pull air past the throttle plate (butterfly).
So you would have to seal the throttle body.

sorry, got my steps wrong. Just did this a month ago should of remembered.

put the vacuum on the side of the check valve that goes into the plenum. that will test all the lines & vacuum canister and check valve.

so your using it to check EVAP system not the intake system:

That isn't the evap system, at least not the complete one. It's still the intake. All you are doing is using the vacuum pump in place of the engine creating the vacuum. The check valve at the plenum is just a 1 way valve so air can't go back into the intake. This is pretty standard way to check for a vacuum leak as well a smoke test.

New update and new codes
 

Changed the rubber boot between the plenum and the intake. Checked for leaks. Then took it for a test drive. Cel came on again after 80km. Car pulls strong, but seems to have a problem on low throttle settings. New codes: P300, 301, 304, 305 and 306.
Changed plugs and inspected coils. Could this be a fuel problem?
Filter perhaps?

P300 is a general misfire code.
P301 is cyl 1 bank 1.
P304-305-306 ia all cyl.on bank 2.

So You have an issue that is causing misfires on both banks.
Could be a vacuum leak.
Could be a fuel problem.
could be an electrical problem.
Could be a sensor problem like the MAF sensor.
Could be any number of things.

Best thing to do is go with a good automotive diagnostic procedure.
That is: start with the simplest things first and work your way up step by step.??

I assume you have done the basics??
Checked battery condition via a load test?
Looked at plugs and coils??
Has good clean fuel???
Good clean air filter??

After that:
Start with a proper vacuum test with a vacuum gauge.
If you know how to use a vacuum gauge for testing you not only can test for vacuum leaks but it will give you a good baseline for overall engine condition.

Greater engine loads and more throttle create greater fuel demand.
You say it pulls strong: does not sound like a fuel issue to me although it is possible. It doesn't sound likely.


If you have something like a Durametric scan tool you could hook it up and look at fuel trims and O2 sensor response to try to determine if you have a lean or rich fueling condition. If you do this could help in knowing what to look for as the issue.

From the info you have provided my guess is you have an air intake issue:
Vacuum leak
Maf sensor issue
IAC issue
EVAP system leak
Something related to air intake

You stated you had air leaks in the intake. you did some work there.
Do a vacuum test with a vacuum gauge it will help tell you if you have fixed all the vacuum leaks.

Or it could be electrical


Lets try to find the cause of the issue.

Give me more info on the car.

Miles?
Is it all stock or are there mods?
If so what mods?
Stock air filter?

So if you start if and let it warm up how does it idle??
What RPM does it idle at?
Smooth with no issue? or lumpy- rough?
Hunting= RPM moving up and down?
If it idles lumpy or rough or hunts, will it smooth out if you hold the RPM at around 2000-2500 RPM?? Do this in neutral and let me know.

Pull the freeze frame data with your code reader and post it.
That will tell me the conditions when the codes were set.

Some more information on the case
 

The car has done 130 000 km.
Stock air filter.
Mods: Plenum is from Pedro with a splitter in it. Throttlebody from an early 996. Stainless steel exhaust and headers. Underdrive pulley. This configuration worked fine until I put it away for two years.
Has changed the plugs, inspected the coils, changed oil, filter and air filter. New waterpump and coolant. Changed a sleeve with a hole in it. Has checked twice with start gas, cannot find any more vaacum leaks.
It was stored with very little fuel in it. Have not changed the fuel filter yet.
Will try clean the MAF and change the filter tomorrow.
The car now idles at around 900 rpm. Up and down maybe 100. When I have driven for a bit the idle seems to rise to about 1200. Then settle down again if I hit the throttle for a second.
At 2500 rpm and above I cannot detect any misfires. With light throttle and below 2500 I can hear and feel less than smooth operation from the engine.
With full throttle it picks up speed fast without any detectable misfires.

Classic intake air issue symptoms.
I believe you either have a vacuum leak.
An issue with the MAF.
Or an issue with the IACV = intake air control valve.
The IACV bypasses air around the throttle body butterfly so the engine can idle properly. They are fairly simple and can stick and hang up.
They can be disassembled and cleaned.

You can try cleaning the MAF use only cleaner spray made for MAF'S
Don't touch any part except the MAF housing.

If that does not work try unplugging it and see if it idles differently.
If it does the MAF is suspect.

If the issue remains look at the IACV.

Also possible is a vacuum leak via the EVAP sytem or the SAI system.

Let me know how you go.

Update
 

Cleaned the MAF. Recalibrated the ECU. Still erratic idle and problems when not under load. Goes well when it got higher revs.
Cel comes back on after a few km. It idles on about 800 when Cold, 1200 hot.
New search for vaacum leaks. None found.
If I disconnect the MAF when it idles it immediately stops.
Also opened the oil filler cap when it was idling. Not difficult to open. But some suction there. The idle jumped up to 1500 With the cap open.
Will change fuel filter tomorrow, just in case.

Are you disconnection the MAF while it is running??? Or disconnecting then starting the car and it dies?

Unplug it with engine off.
Then start car and see how it runs.
If it runs badly or dies then I would say it is starting to sound like the MAF could be the issue.

Usually when you unplug a faulty MAF the car runs better.
But you have those intake mods so I am thinking the opposite will happen because the DME defaults to openloop fuel maps when you unplug the MAF.

So I would check and clean the IACV first. Just to be sure it is not the problem.
No cost in checking and cleaning the IACV.
MAF sensors on the other hand can be a little pricey.

About how many miles did you put on the car with the current intake modifications before you stored it for the two years???

Did you have any issues with it as modified before the two year lay up???

Maf
 

Deleted the codes, unplugged the MAF and started the car. No difference. Car runs, but with the same symptoms as before. Will clean the throttlebody and valve tomorrow. What other possibilities are there? Random misfire reported on all sylinders. No vaacum leak found. Can it be the AOS?

On a stock engine the symptoms your describing:
Idle hunting from low to high idle.
Rough running at low RPM but improves with higher RPM
Those are both classic symptoms of intake air issues.
The three main causes are:
Vacuum leak
Faulty MAF sensor
And in your case because you have a IACV =Intake Air Control Valve on the throttle body.
The IACV.

Then there are other less likely causes like bad valve timing which again is related to the intake air.
So everything I read in your posts says to me there is some issue related to intake air.
I could be wrong but it seems the most likely based on your info.

You also checked the most likely electrical issues and found them good.

Your misfires:
They can be caused by a vacuum leak.
But they can also be caused by electrical issues.
such as fouled plugs
failing coils
issues with the wiring
bad valve timing
bad ignition timing.

A major issue with your situation is that the intake air system has been modified.
The potential problem being:
The DME/ECU is in a stock configuration and is not able to fully adapt to the larger throttle body and larger or different plenum. And different MAF sensor Or Correct MAF sensor for the stock configuration in a not stock plenum.
So it is possible that the Info from the MAF is just not working with the intake mods.

Because you have mods to the intake air system it makes it very hard to isolate problems like yours because the mods are not configured for the DME/ECU

Vacuum leaks:
A smoke test.
Vacuum test with a test gauge.
using starter fluid
None of them are 100% positive tests.
Here is why: You have the SAI the EVAP system and the AOS. brake booster.
They all use vacuum from the intake. the SAI and EVAP have one way valves that are electrically triggered. The valves can be fine but have a vacuum leak issue on the down stream side. So no vacuum leak tell the valve is open.
A smoke test will not show this because the one way valve is close with engine off.

A Test with a vacuum gauge may not detect the vacuum leak because the one way valve may not be open while testing at idle.
They only use vacuum part time.

Yes it could be related to the AOS but you need to do a PROPER test of the AOS.
That takes a special vacuum gauge connected to a modified oil filler cap.
It tests vacuum in the crankcase.
Some people do this by feeling how easy or hard it is to remove the oil fill cap while the engine is running. But that is not a proper test. It is just guessing.

If cleaning your throttle body and cleaning the IACV do nothing to fix your issue. You may want to consider putting the stock air intake system back on and see if that fixes the issue.
Of course if you no longer have the parts that is not an option.

Hope this helps in some way.

Update
 

Have cleaned the MAF, took a short drive with MAF unplugged. Same symptoms. Have an old, but workable MAF. Will try that one too. Cleaned the throttlebody and the idle control valve today. Will put them back on and try the car tomorrow. It ran fine for two years in this config before storage, but will also test it with the original throttle body. I also have the original plenum.
Changed fuel filter today. Just in case. No difference. Changed plugs last week. After the problem started. The old ones looked good. Light grey, no overheating or deposits.
Maybe I shall change the OAS?

Thank you all!

Keep us posted I like to hear outcomes.
It still sounds to me that issue is in some way related to the intake air;)

Update
 

Tried to different throttlebodies. To sets of throttle position sensors and two different idle control valves. Same symptoms.
Hooked it up again to the Bosh Motronic. Seems like I have a lot fewer parameters to view than in a more modern car?
Get some info from the OBD, but little in depht on engine management etc.
This is a professional tool. Any ideas what to look for?
Also tried the Texa scanner. It can not scan boxster 2.5. Works from 2.7 onwards.
Will order a new AOS and change it, just in case.
Any thoughts?

Can you look at:
Short and or long term fuel trims??
O2 sensor signals??
Throttle position sensor signal??
MAF sensor signal??

Camshaft deviation??
Actual camshaft position??

Does it have freeze frame info on the codes??

Also a Vacuum test with a vacuum gauge would be helpful.
Not only the reading of the needle but the action of the needle.

Update
 

I will try to take a picture of the oxygensensor values and other interesting readings on the Bosch system.
A short summary: The car idles bad. Deviating with a hundred or so up and down from about 800 when cold. When hot the idle is from 1200-1400.
Have changed plugs, checked coils, cleaned maf, switched throttlebody with both sensors, replaced a broken rubber sleeve and checked multiple times for vaccum leaks in the engine compartement. Changed fuel filter and air filter, engine oil and filter.
Both old oilfilter and plugs looked in good condition.
Car still throwing random codes on misfire, on different cylinders each time.
It pulls strong when on heavy throttle, but misfires on light throttle and idle.
Next is AOS. Ordered today.
A thought came to my mind. After deleting codes and driving for 70km I hit the brakes hard to test them. The CEL immediately came on again. Could I have a vaccum leak in a brake booster hose or something? Just a thought.