Q: How did you get the M5R2 to mate to your 4.6 Modular engine?
Did you get one of the "bastard blocks" (91-92 4.6L block) that had the windsor bolt pattern?
Or, did you source a different manual transmission (T5 I guess)
I used an M5R2 from a SC. I had to do a lot of adaptin' and, to be honest, I guess it's too much trouble for someone who wants the car on the road fast. I just did it cause I wanted to accept the challenge to myself.
You have to (among other minor things):
cut a small, non-structural part of the block
modify the starter (half 4.6, half 3.8 starter and get a 10-tooth gear as neither the 3.8 or the 4.6 will work)
get a SC driveshaft... the one on 4.6 autos has a beefier yoke and won't fit in the M5R2
Shorten the driveshaft
Enlarge two holes in the 5 speed to 5/8 with good precision
Get a tune and upload it
Figure out your wiring and work out any electric gremlins that might arise from the swap
Fabricate two angle-iron brackets for the lowermost holes on the 5 speed
Fabricate a plate from 1/2" flat stock to relocate the shifter (it'll end up too close to the dash)
If you are the kind of guy who has fun tinkering and solving mechanical problems, this is one hell of a "fun" project
but if you're not that much into headaches, better mate a TR3650 from a 2005-10 Mustang to your 4.6 and be done with it...
If you do get into this, let me know, I might be able to help.