3.8l t5 mustang from a 96 mustang to a 87 2.3l

Get the input shaft and bearing retainer for the 2.3. Then use the 2.3 bellhousing. If it is going into a car that was a manual already you should be almost ready to go. You may have to jumper the neutral safety switch in the 2.3 harness (down underneath be the trans), depends if the 3.8 has one.
 
this has been covered numerous times. Search.

U can't just swap the input shaft. There's a little gear made on to the shaft, and the gear is different between 3.8 and 2.3.

U have to take the 3.8 shaft out of the transmission and have it GROUND down to .590 (stock 4 cyl size), and when you do this, you remove the hardened surface, so it won't last forever. A lathe won't cut it (tried)-at least not with a HSS bit. Replace the pilot bearing but don't drive it in all the way. All SN95 T5's have a longer input shaft than fox body 5.0's, but still about 1/4" shorter than fox body 2.3's. It'll work but not ideal.

Lastly the gearing is different. A stock naturally aspirated 2.3 won't have enough torque to pull 5th gear, period. Mine is turbocharged and it's in boost almost all the time in 5th at freeway speeds, with 3.45's. I put 3.73 in it before I took it to paint so didn't get a chance to run it. 3.90 would be ideal but I didn't have a set laying around. With a n/a 2.3 and V6 T5, you may look at going to a 4.10.
 
It was previously a na 2.3 now it’s a forged bottom end hx35 turbo with holley efi super sniper as the fuel. This is probably a very dumb question but to make up for the short input would it be worth getting the bell housing shaved like an eight of an inch or something where it meets the motor so it would be at least closer to proper length? And will I not need any type of adapter plate it’ll just be my 2.3 bell housing bolted to my motor and the 3.8 transmission case bolted to the 2.3l bell after I get the input turned down?