4T80E downshifting or will not shift

I have the 4t80e transmission in a 1995 Aurora. I just put a motor and tranny back in the car. I had bought the car from a lady with a cracked block (froze) so I had to replace the motor. She had also told me that it would not shift into 3rd gear because somebody that tried to steal the car did something to it. When she took it to a transmission shop they told her it was the shifter cable? When I had the transmission out I replaced the shift solenoids, speed sensor and the TCC. When flooring the gas on the car the car shifts at 6000 no problem. When I am driving it normal the shift normal sometimes with no check engine light. When I take off from a stop sign the next time it will not really shift from 2 to 3rd unless I accelerate 4000 to 4500 RPM )then let off the gas then when hit the gas again it will down shift again into 2nd gear and the check engine light will come on. The light will come on then go off depending if the tranny is working or not. Any ideas? I heard maybe modulator? Anybody know where that is located? Thanks in advance for any help you might be able to provide?

I recomend getting the codes pulled when the ses light comes on. It should be a p07xx code. Pray its not the input speed sensor, that's a tough job. Does it shift hard?

I replaced the Speed Sensor, shift solenoids & the TCC when I had the tranny out. After I replaced the Alternator because it was charging at 17.2 volts it seemed to shift fine but I only took it the car for about 10 miles with no problems. The Alternator still shows that it is charging at 16.2 volts? I think I am going to take the alternator that I took out and get it tested. Does anybody think it might be the BCM that would be doing this? For some reason I am thinking my problem is not done with yet! I am going to take it for a few more trips before I consider this car road ready