Ford M5R2 Noise Problem

I recently purchased a Ford F150 with a 5.0L engine, its 4WD and the body was in very good shape for 150,000 miles.  After driving it about 40 miles per day back and forth to work in has started making noise on acceleration and when slowing down.  I have not removed the transmission yet it’s a M5R2 I have observed transmission fluid leaking from the rear seal, and the rubber plugs on top.  I drained the fluid found it to be brown/black and missing probably 1 to 2 quarts of fluid.

What can I expect to find in the way of damaged components inside the M5R2?

Base on our extensive experience with M5R2 remanufacturing you can expect to find a damaged input shaft and most likely a damaged counter shaft.  This damage is in most cases caused by excessive heat due to low fluid.  You should also plan on installing a new bearing overhaul kit with syncro rings at the same time.Those two parts are identified as item 5 and 32 in our parts illustration