Found this info. Might be helpful. If the Mustang guys use the trans with all their power adder I can see why you couldn't use it with your 390.
TR-3650 used in 2001-present Ford Mustang GT's
1st: 3.380 :1
2nd: 2.000 :1
3rd: 1.320 :1
4th: 1.000 :1
5th: 0.620 :1
Rev: 3.380 :1
Note that in the other TR-3650 applications, the gear ratios are the same with the exception of 5th gear.
Recommended Oil and Fill Capacity
TREMEC engineers have recommended Texaco-Havoline Dexron III/Mercon Non-Synthetic ATF. The most recent Ford owner's manuals specify 3.17 quarts of a non-synthetic Mercon ATF. There has been a significant amount of confusion regarding the proper capacity and proper type of ATF for the TR-3650 which may have a correlation with a rather large number of complaints about notchy shifting, shift "nibbling", noisy synchros, and grinding gears.
I don't like the gear ratios. First is two low and the over drive is to high.
What rear gear ratio are you using? Most Mustang GT have a 2.79.
What RPM range does your engine make its power in?