Thought so. In a PTO driven hydraulic system, the aux PTO shaft drives the main hydraulic pump. Steering is typically assisted by a second pump, engine-driven. The main PTO drive shaft is nested inside the main drive shaft. Inside the housing, this main shaft drives two other shafts; the splined stub that drives your PTO implements, and the aux PTO shaft which resides a few inches the external stub. On engine driven systems, this shaft is covered with a plate. On yours the pump is mounted in place of the plate. There should be a pair of steel lines about an inch in diameter that carry hydraulic fluid to/from the pump.
What you describe suggests the original clutchpack was mal-adjusted to the point where the PTO clutch would not disengage from the flywheel. On rare occasions, an otherwise properly adjusted PTO disc can freeze to the flywheel if/when the the PTO remains engaged during extended periods of non-use, particularly if it's parked outdoors. For whatever reason, your original PTO disc was apparently not releasing. The clutch work you did resolved that issue, because your description now describes a properly working PTO clutch.
//greg//