If you are hearing a hiss -I would follow up on the vaccum line angle,as that would make that car idle fast---i think you said a little over 100 rpm---if that's what you said -that is too high ,.The high idle is what is likely causeing the tranny to slam hard.My lumina manual is in tatters pretty much -but I i am sure that idle should be around 650 or there-abouts.
With the motor swap ,definately try and find the donor car as that car's vin number will tell you about the computer and it's e-prom.
I think you said it said mpfi on the plenum-that would tell you it's multi-port injected -not throttle body.
with the original motor -you need the original e-prom when you change ecm's-so if you swap motors you would need both the donor car's computer and e-prom.
I can't vouch for the accuracy of the information in my Haynes manual but it lists the 2.8 v6 for the 90 beretta and the 3.1 for 91 and later.However the Lumina did have the 3.1 in 90.