Hi Paradox,
The two set screws are designed to pin the clutch body to the PTO shaft. One pins the body onto the key steel and the other 90 degrees from the key way. What you'll find is that the set screws have points on them and as such pierce into the shaft thus making it a tad had to slide the shaft off as there will be a bit of a bur on the shaft that the clutch has to slide over.
You might find that you need a larger 3 leg puller to give it that extra bit of force without any striking involved.
BTW what's wrong with the current power plant ?
Cheers,
BB