I have a 68 Mustang that shifts just fine driving under normal operating conditions. When I accelerate faster than normal (not WOT, fresh motor rebuild) it shifts late running the RPMs way up before shifting. Seems to be more of a problem when the car is warmed up but still shifts a bit late when cold as well. The rest of the gears shift fine.

The car hadn't been driven in the past 2 years prior to the fresh motor rebuild just completed. Shifted fine then… While the car was at the shop for the engine rebuild they replaced the rear seal in the tranny and filled it with fluid. Fluid level is good and looks clean. Could this be a simple filter cleaning issue or am I looking at a rebuild?