I have made some progress on this build. The Command had leaky head gaskets, so the heads came off, and new Kohler gaskets were installed. The hub for the clutch that I ended up selecting is referred to as a "front drive adapter" KH-24-029-09-S. It is almost 4" long, but ended up being just right.
I used the driveshaft flange assembly with bushing from a 1989 1050. The original clutch driver bolted onto the hub adapter perfectly with a pair of 3/8"-16 bolts.
The .500" thick 1" diameter steel spacers were sourced from Ebay, and much cheaper than the OEM Cub Cadet spacers.
It all fell into place. No issues with lining up anything.
A couple of hours of connecting wiring, hoses and cables, it fired right up, and sounded good. I temporarily used the exhaust from the 2206. I am fabbing up the muffler setup. It drove under its own power for the first time in a long time. The clutch worked perfectly, with no slippage, noise or chatter. There is no vibration at any RPM. It's as smooth as butter. I ran it for an hour and no oil leaks.