I have not torn down the hydro system, but I have added the cooler package and replaced the oil and filter a number of times. The only time anything strange happend was after the first oil change. When I started to move the machine, it made a strange noise. This quickly went away and everything was fine. I think that I did not let it idle long enough before trying to move it and the oil had not fully circulated leaving some air in the drive motor. I would check with your scag tech.
On edit. the machine is a 1999 turf tiger