6.0 swap with 4L60E not shifting

[gbenfield]

I'm about finished with my 48 COE, but having a transmission problem, first of all just in case it could have something to do with it. When it's cold it will start right up but will not idle on it's on for about 30 seconds then it's fine. I can take off in first and shift manually up to 3rd ( won't go into 4th). If I start in drive it is in safe mode and starting in 3rd. I'm getting 3 pending faults of P0740, P0753 and P1860. I fell like it is in the wiring, not getting a signal from something telling it to work, I have power to pin 33 from normally closed brake switch. Ive got power on pink wire to tranny. I'm not sure what other wires to check, also it's a after market wiring harness.