2nd gear not working, 4th working after engine swap HELP plz

Hi, My name is Maurice and i have a 4l60e hooked to a lt1 (95' from a donor impala ss) in a 89' Mustang. The tranny/engine combo just came out of another car (not the original impala) and all gears worked perfect. I did the computer tune myself including the tranny changes, but after the swap...

The car goes from 1st to 2nd (according to the computer only) but CONTINUES to accelerate as if its still in first!

Then the car when you let off (because it will hit the rev limiter in second because its really in first) shifts to 3rd and drives fine in 3rd.

Then when it makes the 3rd to 4th shift it seems like the rpm barely dropped it acts like its in 4th, BUT the rpm doesn't match the gear ratio calculations i made and the rpm change from 3rd to 4th is only a few hundred rpm. 3.55 rear end, 225/45r16 tires and 2500 at around 60 mph (not exact because i don't have the speedo hooked up yet)

SO i have so far -

Check for codes - only came back with code 83 (tcc solenoid code)
Check the wires - yellow/black and light green (solenoid 1 and 2) at the ecu are making connections to the tranny (even Checked inside the pan at the solonoid)
Check the solenoids - removed and cleaned them (soaked and sprayed air through them) then check resistance (around 22ohm) and hooked 12volts from a battery to them (clicked each time)
Checked the output from the computer at idle (only 1 solenoid output was on at idle in park)

I then hooked a pair of switches to the 2 wires and by manually actuating the solenoids i got the exact same results!!!
Also when manual shifting the car the tranny lunges when rolling and going from 2nd to 1st, yet the car is still in 1st either way it just makes the downshift lunge as if it has increased in rpm yet it doesn't

Also the Tranny has around 50,000 miles.

Any help is appreciated , Thanks!

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89' Ford Mustang 5.0 - 95' Lt1 Fully forged internals (eagle crank, H beam rods, srp 8.7:1 pistons), 4 bolt forged splayed mains, comp cam/springs, Aje K-member, Flaming river manual rack, 3.55 gears, 2" custom wide body setup, Black Cobra 16"