Jason you can get the gaskets and seals from any Cub dealer and probably any of the sponsors above. If I remember right the seals on the stub shaft and trunion shaft are different on the older hydros than the newer hydros.
When I put a hydro back together I have a small container with hydro fluid and dip the parts in it or use a spray can with hydro fluid and flush all the parts. It can't hurt.
When I reassemble the swash plate I remove all of the pins from the swash plate, then put a pin in the stub shaft and one in the trunion shaft. Then insert the stub shaft and trunion shaft into the hydro and the swash plate. Looking down on the swash plate you can line up the shafts with the hole in the swash plate. Once they are aligned drive them in 1/2 the length of the pin and they will be centered on the shaft and the swash plate. On the side with the two pins drive the second one in 1/2 the length of the pin from flush.