For a NA 2V, do a stock rebuild. You can get a fresh rebuilt 3650 for $1060 shipped to your door. That is what I did in my 98 but there are a few "gotchas".
To do the swap you will need:
-Stiffler's tubular crossmember for 96-98 GT with t45/3650, installed with no spacers under the trans mount
-79-95 trans mount
-3650 shifter
-Dallas Speedcal
Crossmember is because the 96-98 stamped unit will not physically clear the bottom case of the 3650. The 79-95 mount is because you have to install the crossmember in the rearmost configuration and the 96-98 style mount has rear offset bolts that will not fit in the slots. 3650 shifter is obvious and the Dallas Speedcal is to convert the 99-up OSS speedo signal to 98-down VSS.
For the T-56... not worth it unless you need that 5th gear. Yes 5th gear. 6th gear is the same in the Cobra T-56 (.62) as 5th gear in all 02-04 3650s. 01 cars had .68 like the T45s did. Another issue with the T-56 if you get one of the used Cobra jobbers for $1500 is have fun with that 2.66 1st gear in your 2V. Better invest in some 4.30s or better yet, 4.56s unless you are going with a positive displacement blower. Custom ratio T56/Magnum is the way to go for a 6 spd (wide ratio 1-4 and then close ratio overdrives) but is overkill IMO and ridiculously expensive.
Your other option is to get the t45rebuilt by
www.thet45source.com which will run around $1500 plus shipping both ways.
I already had a speedcal and the shifter was cost neutral after selling my tri-ax and picking up a used 3650 version. I am into my 3650 for appx $1250 and I still have my T45 core it replaced. Shifts great up to 6k no problem and the .62 overdrive is great with 3.73s on the highway while retaining the 3.37 1st gear in the t45/3650 to get the 2V off the line.
Pics
Old
New (prior to replacing a cheap parts store rubber 79-95 mount with the poly one)
Cruising with 3.73s