Transmission making noise - opinions requested

1999 996 Cab. About 97k on the clock. Haven't had the car too long. Did a lot of research before I bought , but got such a great deal on this one that I ended up just doing a thorough inspection and buying the car without an official PPI. (long story, but I stand by my decision with this). Anyway, everything seems good on it a month later except one little nagging issue. In 2nd and 3rd gear (predominately), between 20 and 60mph, and only when accellerating, it makes a decent amount of gear noise. Compare it to the whine of a supercharger only you can feel it in the gas pedal a little bit. Everything else is perfect though. When you stop accellerating and back off a little it goes away. Same with gear braking, not much noise there either. Certainly nothing at a stop or out of gear. Only when accellerating in that window stated above. At first I thought it was just "one of those things" that a porsche does. Like my Ducati... makes a RACKET because of the dry clutch but that's perfectly normal. My old S2000 had lots of normal noises too. But now, after reading a few other posts, I'm worried that I might have a worn pinion or main shaft bearing inside the tranny. Based on what I've described... does anyone know how severe a problem I might have here. If any? What I mean to say is... if I drive this thing another 1000 miles what are the chances (vegas odds here) that I'll screw something up even more. I'll add too that the car shifts very smoothly warm and cold, never "grinds", and never pops out of any gear. Aside from the gear noise/whine/feeling in the pedal in 2nd and 3rd while accellerating, it seems perfect.

I didn't say it but the car is a 6 speed manual by the way. One more thing I'll add also. In all the service records given to me (dating back to 2002) it doesn't appear as if the tranny fluid has ever been changed. At 97k it's a few miles past due (due at 90k I believe). So I intended on changing it in a week or so. Will that factor into anything?

I just replaced the output shaft bearing and with a new bearing the transmission is dead silent, so something's up. Swing by a couple good shops and have technicians ride along with you to pick out the noise. Edit: At this point it could be who knows what, best to just get it checked before wild speculation kicks in--no reputable shop is going to charge you to hop in the car with you for a minute.

Would you mind sharing what this cost you to fix? Parts and Labor separate (I intend on doing most of the external work myself).

Unless you've got a 30 ton press all you can do is drop the transmission and take it to a shop, the gears / bearings are all press-fit on the shafts.* Total I payed $2750, about $1800 labor. I had the main and secondary pinion shaft bearings replaced, along with miscellaneous stuff (seals, new gear oil). Dropping and putting the transmission back up was 8 or 10 hours, so you could save that. I don't have the invoice in front of me so I can't be exact, but that's pretty close. * - Just a note. Once you've taken the gears off and put them back on once after manufacture, you can't work on it again. Apparently the whole procedure is pretty stressful and the parts won't hold up past that one repair, so it's worth it to inspect everything and replace things that may be an issue.

Turbodriven, My car has the dreaded worn pinion shaft bearing noise. It is way loud and doesn't matter which gear you are in. It is especially bad in 3rd-6th gears. If it is intermittant as you say in your post i'd wonder what is really wrong. Pinion shaft bearing will make bad sound whenever gear is engaged. On acceleration or deceleration. Mine is worse in 4th gear at lower revs, but makes bad noise anytime it is under a load. Price i've been quoted for replacing bad bearings is close enough for me at least to just pay the additional money to have the whole unit blueprinted and repaired. Just my .02 worth.

I have a 2000 C4 cabrio and I take down the tranny because the Main Pinion bearing fails. Reading about the problem I found that the failure is cause because it is sealed and the grease fail due to heat. I am looking for a replacement with out the seal. Any after market replacement?