This winter I did a lot of work to my 2001S. IMS, RMS, aluminum flywheel, sport exaust.. First drive was great short 130 miles sunny day with top down. Pulled back into garage and heard funny noise coming from rear. traced it to internal transmission. Any one know where to get better bearings for a decent price.

 

Call California Motorsports

 

Sounds/ looks like my 2000 S tranny 10 years ago. Replaced it with a rebuilt unit, never tore it down that far.
Was the noise localized at the tail (rear) end?

 

Not clear from your brief note and photos what you believe the source of the noise is inside the transmission. The fuzz on your magnet is not an obvious concern: it's normal to see a little debris as parts break in, shifts are made a bit too quickly, etc.

I would not just replace the bearings when rebuilding. I'd go through the whole transmission and get everything set up to factory / Getrag spec. I am rebuilding these transmissions with correct bearings, shims, seals, etc., setting them up per Getrag's spec. The original bearings used by Getrag are fine, and I don't think there's such a thing as better bearings, unless you're referring to "better" in the sense of "less worn." California Motorsports, as mentioned above, is rebuilding as well and they do excellent work. Good luck,

 

Or just install a stock flywheel.