I finished up with the 129 lift upgrade tonight, along with some minor engine work and steering and hydro linkage repairs and upgrades.
Although it was mostly a "bolt in" swap, it didn't mean that there weren't a few modifications and tweaks to get it to work. Fabricating the left hand lift handle support was one that I knew in advance, and turned out to be no big deal. Here are a few things I did have to tweak and change to make things work well.
I had the driveshaft from the 1650, along with the rear rag joints, but not the complete front coupler, as the parts tractor was engineless. I ended up shortening the 1650 driveshaft slightly, and had to drill an additional hole in the driveshaft to make it work. I might have gotten away with changing the spider on the hydro pump to the 129's, but I like the heavier parts from the 1650. I used the front coupler setup from the 129.
I had to do some gentle bending of the hydraulic lines from the pump to the valve body, in order to clear the hydro control linkage.
I had to rework the clamp which goes around the lift lever shaft to tighten properly, It had gotten stretched and I had to widen the slot a bit.
I got the engine back in yesterday and resolved the drive line issues, today I installed the gas tank, generator, seat pan, and finished hooking up the wiring, and filled the transmission with Hy-Tran.
The engine started right up, and the lift worked well. After assuring myself that there were no leaks, I took it on a test drive. The trunion repairs seemed to work, it held speed well going up and down hills in the yard without having to fiddle with it too much, I didn't even need to adjust the Neutral position. I put the mower deck on and tested it out, it worked as I expected it would, but final adjustments will have to wait until morning.
Thanks to everyone that's provided hints along the way.