Final troubleshooting for Ford 460 motorhome, advise?

So the slow takeoff from a stop is the same before and after the engine work? If so then possibly not the transmission. You can try shifting into 2 and starting out from a stop. Unfortunately some transmissions will start in first gear anyway. But it will only upshift once into 2nd gear so you will know that it started in 1st which answers the question.

Do you have any idea why it overheated in the first place? If there was a constant misfire it could have overheated and melted the cat.