The nose that goes into the crank bushing is too short on an FE tranny, as you have been discussing...
Some things I'd like to add:
You can use the FE tranny as is if you get a long crank bushing to reach out to the short nose.
You can get them to adapt this tranny to an SBF, but it takes some looking. Dan Williams would probably have one.
You say the tranny is 31" long?
Sounds like a long shaft toploader... Not saying it can't be adapted to a Stang, but no Stang ever came with a long shaft tranny, so you will have to fabricate alot of parts and hybrid parts from long shaft cars. Alot of guess work.
There seems to be alot working against you. In the end you will have just as much money in this tranny as you would spend on a short shaft/wide ratio tranny that would be much more user friendly. Install would be much less of a headache too.
Use your own driveshaft and crossmember, use off the shelf Stang shifter and intall kit, and save front bearing problems by using the SBF input.
What is wrong with a "25 spline"?
I don't know the differences between 25 and 28 specifically, but I do know the lowest rated toploader is said to be 500 hp.
Is the 25 spline the SBF tranny?
If so, it doesn't matter much...
Ford did 250 7000 rpm clutch dumps on slicks with a drag modded SBF in the late 60s as a publicity stunt for the toploader and never broke it.
Sounds pretty strong.
Dave