New Transmission Cooler
 

I had the transmission built on my 2000 trooper a year ago. I noticed some slippage in first gear. At the same time I had a alternator problem and had it replaced. I took the car to the transmission shop. They said I may need a transmission cooler and a fluid/filter change. After that was done, the first gear slippage was gone but now there is a delay or slippage between second and third at high acceration. If the shop didn't top off the fluid when I had the cooler put on, would that cause the slippage between second and third? Or could it be something else that could be fixed without another rebuild?

Possibly, but checking the trans fluid level is a major PITA on these.
But that would be the first thing to do.
If its not that and its internal, I'd go somewhere else
That should have been addressed the first time