Tranny swap now having issues

Ok so I have a 99 gt. I pick up a supercharged motor and tranny out of a wrecked 2000 gtp, unfortunately I couldn't get the ecu and wiring harness out of that car. So my stock tranny has been slipping so I decided to put the HD tranny in (I'm doing the rebuild of the l67 block in the mean time) I put it in and everything works fine except I have no 4th gear no overdrive. Then I find out the gear ratio is different from the HD tranny and the stock gt tranny and that's why it won't go into overdrive . It just stays at 3000 rpm at 70 mph I was wondering if they is a way to get my stock ecu to work with the HD tranny.

Tune it...HPT or DHP. If you don't have access, ask around. Chances are someone in your area can hook you up. Otherwise, you could always get a tuned PCM from a vendor such as ZZP or Wbodystore.

I'd be surprised if the gear ratio is why you aren't getting 4th. You'll need it tuned for the ratio either way. But likely the 4th hub shaft splines went south for the winter.