Automatic Transmission in Manual Car

Okay, so here is the problem, I had a 95 formula with auto tranny that i wrecked back in february. The motor was still good and I had recently put invested alot of money in the motor and accessories, (a/c, alternator, radiator, fuel pump), so i decided to put the motor and tranny in another body. so, i bought another 95 formula body, but it had previously been a manual set-up. I put my motor, and auto tranny in it. My computer was trash but I got another one from a 95 camaro with auto tranny. Now that everything is in the car and running, when i put the car in drive, it goes into and does not shift from 3rd gear. I can manually shift 2nd and 3rd, but no 1st or 4th. reverse works as well. My speedo doesn't work either. through research I have found that usually means that the tranny is in "limp home mode" because of an electrical connection problem. I figure that is probably a problem caused by something in the wiring harness that is different between the auto and manual. I know that there is a switch in the shifter that i dont have plugged in because there wasn't a connector for it in the manual wiring harness. Is that what is causing this? Also is there an automatic tranny relay or fuse that a manual car wouldn't have? Or do you think it is some other problem entirely? I'm stumped. Please help.  

follow the codes....    post the codes...

do you have access to a scan tool that will display live data?????  

i take it that you have a wiring diagram for the engine controls...

are all the grounds hooked up??????  sometimes people leave them off thinking they are not important..

you may end up checking every circuit... with an OHM meter...  and the ecm unplugged..

was the engine harness from the old car damaged????    what did you do about the connectors for the transmission ... it is a computer shifted automatic transmission..

do you still have the old car body????     you might want to see about seeing if the replacement ECM needs to be reflashed to your engine specs...  you will need the VIN number from the old car to properly reflash the ecm... or it will become a stick shift ecm.. as the vin number on the new body is a stick shift version..