Most internals will swap, but there are certain "rules" to follow.
These items do NOT SWAP:
None of the forks, or fork linkage
None of the three main case parts.
Your fifth gears will need to stay as pairs:
A 2002-2004 has the 0.62 ratio and a 2005-2010 has the 0.68
A 2001 TR3650 has the 0.68 fifth gear as well...
Pick the ratio you want.
The gear sets are all the same tooth count and ratios but they changed the angle of the teeth on SOME of the gears in about 2004. If you look closely at the counter shaft of an 01-03 where first and reverse mesh with the counter shaft there is no step between the two areas. On the 2004-2010 version there is a small step between the two gear heights.
The gears that are different between these two sets are:
Reverse main shaft gear
Reverse idler gear
These four items must be all from the same style gear set. You can see that the tips of the gear teeth are flat where they were pointed before and are pointed where they were flat before.
The bearings and races are all the same except the 2005-2010 has a tail flange bearing and the 2001-2004 has a tail yoke bushing.
You will need to tear the main shaft down completely, as the shafts themselves are not the same. This takes a press and some pullers.
1965 5.0 Coupe /MAF/EFI/Astro A-5 T-5/B303 Roller Cam
Mustang Manual Transmission Specialist