Linkage (Make sure it is engaging into each detent on the trans correctly) Did that.
Filter (Be sure it's the right one for the year of the trans and installed correctly) The new one is identical to the one that I removed.
Converter (not put back in correctly and damaged the pump) I made sure that it was seated correctly before mating the trans to the engine and bolting it together. The first time I tried to line it up it hadn't seated correctly, so I removed it, fixed it and re-installed it. I started to bolt it together, but realized it wasn't right after trying to put two bolts in.