goto junk yard for 400 yoke (will be fine into 10s, maybe 9's), or buy at Moser if higher strength is needed. One note on yokes, there were two (or more?) versions made... get the one that fits your particular outputshaft and tailhousing bushing. THe main difference is the wall thickness of the yoke, requiring a larger tailhousing.
Crossmember to mount hole needs "oblonged"
For manual, either get a manual VB (FULL manual or TB) or a shift kit.
I dont really think you can tell that accurately since there is going to be many factors affecting the install including engine settle, which is hard to predict. Just bolt the tranny in, jack the back of car up, and swing rear with DS in (but not bolted to rear), Check for AT LEAST 1/4" in out movement into tranny tailhousing at the "tightest" point of rearend swing. The tranny install is easy, prolly take less time than "calculating" everything else.... besides, its gotta go in anyway.