I doubt the PTO problem is related to engagement, you questioned... given the other symptoms of wierd steering and poor performance with the hydraulic SCVs, I'd say you have a hydraulic issue somewhere. If I'm not mistaken, both PTO engagement and braking are done via the hydraulic system on these.
You mentioned the "gear pump"- I'm assuming you mean the transfer pump in the transmission that supplies oil to the main pump. When I had one of those fail, there was no hydraulics whatsoever.
I think you need to measure output from the main pump first, and then work back from there.
Checking the sump screen and filters would also be prudent before going too far.