1. I will need a cable operated 3.4L 996 throttle body
2. I will need to add wiring to the dme to run the varioram changeover solenoid
3. I will need to use my current 5 speed flywheel.
4. I will need to have my Bosch 5.2 DME software changed from 2.5 to 3.4L, which should work fine with the 3.2
Both the 2.5 and 3.4 used the same MAF (996-606-124-00), but in different diameter housings. If you go to a 3.4 flash, you'll need a larger MAF housing to get your AFR's right.
Now my questions:
1. Will the 3.4 throttle body fit my 2.5 crossover tube and will that in turn fit the 3.2 plenums? If not, will I need to use a 996 (99 model year) crossover tube? Will that fit the plenums?
The 3.4 TB will not fit the 2.5 intake. The 3.2 stock TB is 68mm. The 3.4 is 74 MM. If your 2.5 has a 68mm TB, then you should be good with that, but... the 74mm TB will add some power. 
2. I have fabspeed race headers on my 2.5. Will they fit the 3.2?
The bolt pattern fits but I believe the diameter is a bit smaller. I know the cat pipe diameters are smaller.
3. Can I use the stock 2.5 MAF? If not, what replacement is necessary?
The airbox did not change, so that should work.
4. Intake tube. Is the spectre flexy hose the best option or is there a better choice for this setup?
build your own intake from solid plastic tubing. Airaid UBI Custom Intake Systems & Components | JEGS
Thanks for any help you guys can provide.[/QUOTE]