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Car is a 1990 Cavalier with the 2.2l 3 speed auto. Transmission was working fine before the radiator cracked when my wife was driving causing the car to overheat and warp the head. Had the head resurfaced and put on new gasket and put everything back together. Now it will not shift out of first after I put it all back together.

Fluid levels all seem to be ok. No leaking any where.
It appears all sensors are plugged back in
I am pretty sure all the vacuum lines are connected properly.
Car starts and idles fine.

What could I be missing?

I would check your TV cable first. These get loose over time and can start to make the transmission shift incredibly strange, late or not at all.

I'm not sure how they are setup in these TH125's but on my truck transmission, I was once able to fix a similar issue by slamming the gas pedal to the floor, with the key off, engine off. This loosened the sticky TV valve (that's redundant, because TV stands for Throttle Valve LOL) inside of the valve body.

Either way, it sounds like those could be your problem.

Ya you have a cable issue.
If it has one of those goofy boxes that the cables run through they can get screwed up pretty easily.
Just double check everything and make sure everything is connected.
On the TH125's the cable controls everything.

Thanks. I will check it when I get home tonight.