mer10z

I have a 1uzfe from a 92 sc400 in my 4runner and my mechanic friend and I are trying to get it running with a a340f transmission. The 2 shift solenoids are connected correctly to the ecu but the truck never shifts out of 1st gear. If I remove the wiring harness I can manually shift to L, 2, or D and get 1st, 3rd, or O/D that way, so I know that the transmission is fine. I think my friend said that we are using the lexus speed sensor in the tranny so it should be getting the right speed. Are there any other things that we should check into or some diagnosis ideas? We're kind of stuck right now and any help would be greatly appreciated.