Ok guys need some help... Losing my mind with this one.

I completed a LQ9 and 4l60e swap into a 1960 Chevrolet Kingswood stationwagon. Car runs awesome, but I had some problems with the transmission. I will try to break it all down for you...

First, on maiden voyage... Trans shifted fine from 1st to 2nd, but just rev'd up in what should have been third.... Normally I would just say that the 3/4 clutch pak is gone.... But I have a few questions for you guys befor I go hank this thing out.

Next I disconnect the electrical connector from the transmission to put it in "limp mode"... Trans did the same thing.... Good first to second.... No third.

However... When I hook it up to HPTuners and shift it manually the shift selector states...
1 when it is in 1 gear
2 when it is in 2 gear
--- when it is in 3 gear
--- when it s in OD

Doesn't make sense to me... It's like the transmission does even see 3rd and 4th.

More details.... PRND selector connector is not hooked up on driver side of transmission... Didn't think it was needed for my swap. VSS seems to be working correctly, but willing to test it if you guys think I should. I'm lost guys... Really can't afford to spend anymore on this swap, but can't keep riding around in 2nd gear! Any help or suggestions will be greatly appreciated!