Final troubleshooting for Ford 460 motorhome, advise?

No need to remove cat for a brief test, just loosen upstream bolts and break apart to create a small gap, say 1/4 to 3/8 inch. You may have to cut the bolts and replace with new.

Try starting out in second gear, 2, and 1, and shifting from 1 to 2 at speed, there should be a big difference in acceleration and shift points. The transmission linkage may have been bent during engine removal.