4L65E won't shift under wot or downshift

I need help guys, I'm beside myself. This is a Jasper class 2 which was rebuilt with even better parts. I'm essentially at stock power levels. Even with the stock tune, I'm having issues. When I am cruising and I kick it down into 3rd it revs up and won't shift until I let off. Then it clunks into gear. I am thinking at this point it isn't software related. Supposedly the trans has the "corvette solenoid valve?", upgraded drum, shift kit, and hd clutch packs. When I first installed this trans, i was driving and the oil cooler line blew off. I had to drive it because I was on a road where I couldn't just stop. I ran it completely out of oil. I filled it up after fixing the line and it seemed ok. The torque convertor is stock and came with the trans. Any ideas? When i installed the convertor it seemed like the gap was a bit much between the flywheel and the convertor pads, but I didn't shim it. If the convertor is not seated deep enough all the time, could that cause these issues? Any help much appreciated. After beating on the car when i go to shut it off there is a tire chirp like sound that comes from the trans. At the track it goes through 1st and 2nd with hard shifts but then won't go into third unless i let off.

is it tuned? if so can we see it. they have some funny shift parameters factory that would cause some of that. running it out of oil did you no favors, causes quite a bit of damage.