Nothing wrong with a 460LE. Built properly, they handle the grunt fine. Programable for shift points and over-run are a bonus if a programmer is available.
What were the clearances for the shafts (end play) and clutch packs?
A lot of "non auto" shifts happen after a freshen up or rebuild. Line pressures are higher when manually shifting. When it automatic (D), it doesn't produce the same pressures and the valves don't see what they want and the computer is not going to respond to the load the band for 2nd and 4th and apply pressures for clutch pack stacking.
Clearances are critical as a starting point.