Agreed but it is usually the 2nd gear synchromesh and dog ring that wears on the 6 speed.
That is why I suggested a good used gearbox and linked the GBox/CMS service of repairing the dog ring instead of replacing it.
http://www.gboxweb.com/dogring.html
http://californiamotorsports.net/collections/cms-custom-shop/products/porsche-asymetrical-2nd-gear-dog-ring-repair
Pinion bearings are around $480 !
As these cars accumulate 80k++ miles we'll read more of these problems with the 6 speed.
Here is a page from Pelican that may clarify:
http://www.pelicanparts.com/catalog/SuperCat/1048/POR_1048_TRANSM_pg3.htm#item10
Auto Atlanta has the clearest diagrams of the parts layout:
http://www.********************************************.com/results.php

FYI - your second link is same as the first, looks like you intended something different.

Thks, fixed,I hope

Finally have an update after a longer than expected time in the shop.

I am picking it up in the morning on my way to work, and will provide more details on how it shifts etc, but here is a quick update.

First off, they replaced the clutch (including pressure plate and slave cylinder but not the flywheel as that was ok).

Then they did some work specific to the 2nd gear itself - broke down the transmission and replaced several parts (I have some of the specifics written down at home, and will get the full list tomorrow). They had gotten shipped the wrong part which took some time to correct, and then after re-assembly and test driving last week noticed an issue with a noise at higher speeds. They dismantled the transmission again this week and had to replace another part (a bearing or something similar, again hope to have specifics tomorrow).

But at this point mechanic says it shifts smooth and quiet, so I can't wait to find out for myself.

Been longer than anticipated, and cost was more than I hoped / planned, but if it's fixed right and gets me years more of driving pleasure without worrying about the 2nd gear issue it will be worth it.

"They dismantled the transmission again this week and had to replace another part (a bearing .."
In other threads on this subject we usually have a 'while you are in there ' list. New bearings are inexpensive(unlike all the other parts) and are a no brainer because they are 'sealed-for-life;' - like the IMSB is ! The bearings are not expensive but they are difficult to remove and replace as I mentioned in a previous post.
That was embarrassing for your gearbox expert?
First they don't replace the 2 (?) bearings that are known to be suspect and Second ,they did not do a high speed test of their work. Lets hope they filled it with the correct fluid?
BTW for those who haven't read previous threads on bearing failure in the 6 speed , the test is simple.Stick your finger in the drain hole as far as you can and slide it around the bottom of the inside of the gearbox case. Careful, threads may be sharp. If you find greasy sludge there , it is because the seals on the bearings have failed and their grease has leaked out. The bearings are above the oil fill level and the remaining failed seals seem to exclude the splash oil, so ironically the bearings suffer a lubrication-related failure.Noise and the aforementioned grease are the early warning signs.
I have never found an expert explain why we don't remove the seals from the replacement bearings and allow oil mist/splash to lubricate them - or source bearings with better quality seals.
It will be very helpful to see the details of the work done and try to learn something for those that follow.
You did not mention the miles on the gearbox. This is usually a 90k miles+ problem.

These 6 speed boxes are quite troublesome especially if tracked. Some of the needle bearing cages are plastic! I had no idea how hot the oil got when on the track (ignorance is bliss) until I started monitoring the gear oil temp. Before I improved the cooling with a ducted fan, even with a pump and small radiator, the temps often exceeded 260 degrees. After spending close to 8K for a rebuild, I sourced a low mile box for a spare.

I have 150,000 miles on mine (bought a year and a half ago with 115,000).

I believe he replaced one bearing the first time and after doing the high speed test and hearing the noise he said I would not have noticed but he wanted to fix it right.

He did apologize for the delay and his mistake (not replacing both bearings at the same time). I'm OK with that as long as it's done right in the end. He could have just given it back and if I did notice I would have had to bring it back which would have taken longer. He did come recommended as well.

I will update once I get to drive it myself tomorrow.

Deadeye,
Interesting suggestion to cool the oil. Have you posted a DIY for your cooler on 986 or elsewhere?
We really need a simple+ effective set up for fast road use
I considered it but was daunted by this description- perhaps yours is simpler?
Gearbox Oil Cooler Installation Detail and Review.... - 6SpeedOnline - Porsche Forum and Luxury Car Resource

My install is not nearly as well designed or executed as the one in your link since my boxster is only driven on the track. I will take some pics next time I'm at the shop. It does envolve quite a bit of plumbing, wiring for the pump and pancake fan, and modifying the case for the AN fittings. Not sure it would be worth the effort if you don't drive on the track.

Picked car up this morning, can definitely tell difference with the clutch - pedal effort much less.

Mechanic showe'd me the old clutch and pressure plate, and pics of the transmission inards when he had it apart. Second gear teeth were rough (not sure if that is right word or not). Cost ended up being less than estimated, he gave me a reduced labor fee as it took longer to complete.

Aside from clutch itself, gears seemed less notch especially 2nd. Will get a better sense of it on my drive home tonight.

Ride home from work went great. Smooth shifting all the way.

Was nice to drive the Boxster again.