is this a tranny code? if so anyone know what it means

Yes, its related to the trans.

Code: U0100
Modules: TCM
Description: Lost Communications with Engine Control Module (ECM)

did this code happen when u accidentaly pulled the pto...if so maybe thats why it slowed down...it stopped communicating with the tranny and told it something else was going on...i cant think of how to put into words what i wanna say but even so it would make since because you can drive a watertruck with the pto on...also you have to push the clutch in to engage the pto unless u just grinded it in...who knows....try and replicate the problem like u did last time and if it pops up thats what it was...

fixed chaffed wires by the alt and mass air flow sensor

thanks guys