Rebuilt tranny still giving me problems

[Driftersdr]

I spent 2800$ to have a reputable local shop rebuild my tranny. They said they had a bunch of problems with it but finally got it done. Someone(at the shop who blamed it on me) ran something large over and destroyed my tranny pan and did damage to that side of the car so I drove it with no tranny fluid for about 500 miles not knowing it. Took it back and said fix the pan and fill it. They did this. I'm still having bad clunks when I give her a lil kick in the butt. BAD clunks. I took it back to the shop and they say its all good. Sometimes when I drive before it shifts it revs a bit before the shift, sometimes when I stop at a light it doesn't shift back down to first so I start off in third gear. I'm exhaust with this damn thing. For someone who makes 9$ an hour, 2800 is a lot to put in a car that since buying I've just now put 5000 miles on.(Bought over a year ago) Maybe IPT will read this and help me? I have a warranty with all ATRA shops but I want to get this fixed, I KNOW the tranny isn't right and I'm getting no help with this. Does this sound like a normal rebuilt tranny? It really clunks and it seems like it doesn't shift right 9/10 times.