Going into this I was afraid that things in the trans would need to be re-shimmed and such. But I took the two shafts from the transmission down to the dealership and talked to the trans guy. What he told me was that if you are replacing either of these two bearings (see photo) that re-shimming is unnecessary. Also these apparently are common bearing to fail, the top one especially.
An hours worth of labor later ~$85 and the trans guy at the dealership pressed my old (good) bearings off the old input and output shafts from my blown 2nd gear trans, and onto the shafts of the replacement trans I got this summer.

I am weary of advice that people that stand to capitalize on my mistakes give me so I waited until now to post my findings. One week of hard, varied driving has passed since I have done this, over 200 miles. High speeds 100+. Lots of low speed high RPM snow drifting around town(I deliver drugs for the pharmacy I work in) TONS OF DONUTS in the snow, and so far so good.
I just wanted to let people know of this low(er) cost option for transmission bearing replacement that people with the will to drop and crack a transmission can achieve themselves without needing to have lots of trans tech skills (this was my second time in a trans, didn't have a factory service manual either, just a few scans for the torque specs)
I'm glad I had an old blown trans to pull the bearings from. I almost had given it to Doug Vincent, then this repair would have been at least 300 more for two new bearings. The bottom one is ~$150 on subaruparts.com. I elected not to reuse the stake nuts and had them put new ones on ~$15.
Remember, this transmission isn't completely full of voodoo magic that only dealerships and trans shops can summon spells for.
update 1/11/09: still holding together, after 2000 miles.
update 10/10/09: still holding. just bought a trans for 70 dollars with same problem I plan to fix it myself again.