Well the tractor broke down in the woods back on August 29th and was finally back to work Saturday October 12th. Just 44 days :) The splitting of the clutch housing and transmission did not take that long to identify the problem as the splines on the HDT input were stripped.
The major parts replace we're the HST Shaft, coupling and main shaft. A few bearings including a new clutch bearing were replaced as matter of convenience. The clutch plate had excessive spline wear and was replaced. This was also a good time to access the steering hoses. All in all parts were about $1400, I did end up with some extra orings and replaced some hardware that was rusted.
The first time the tractor was put back together an started, we had issues the the gerotor pump was not pumping oil. This was caused by two issues, not priming and the housing being installed 180* out of position. I recommend that once you have the HST installed, prime the system by positioning the small pipe from the hydraulic filter (lower large vertical filter) in a vertical position and turning the shaft of the HST clockwise as viewed from the front. Oil should pump out from the left side of the midcase.
I will try to post some tips and pictures on priming the HST hydraulics, but if you need help on this project or priming contact me.
I also highly recommend checking the torque on the 16 engine mount bolts. 2 had already fallen out and several more were loose.
I also want to thank Jared at Harbor Saw and Supply in Hoquiam WA, he is my local dealer that i chose to order my parts through. He supported me after hours and on weekends to get the parts order correct.