Follow the hydro bypass rod back to the hydro transaxle and look at it and push/pull it back and forth and see if it has full travel. Check the other side for comparison if needed. Make sure no debris is blocking free travel of bypass rod.
Kinda doubt it if the condition existed before the bypass was engaged.
Sounds like it is time for the ZT-3100 to completely rebuilt or replaced. The high whine is likely the unit cavitating from wear. This can be caused by worn out oil, low oil, or water laden oil. The pump faces are separated by thin layer of oil. When there lack oil surface tension the metal pump faces wear grooves into each other. Once this starts it only gets worst over time as the metal grinds away and contaminate the oil. Basically the fine particles acts like sandpaper until the oil filter removes them.
Oil to be used is SAE20W50 Synthetic with Zinc and an anti-foaming agent. Actually I think some Moly may helps things as it re-coats metal surfaces. It is something I haven't tried on a Hydro pump yet as I prefer to do this on one of units that having once customer premission before change out an unit.
