Retail $.....
The retail value of the ski in excellent condition is about $4500 according to Kelly's blue book. But with the engine knock, I'd consider dropping $1000 for a new engine. That's not counting labor, I'd do it myself. With labor, it would be a bit more. If there are any defects (rip in seats, dings, damage, etc...) I'd deduct as I went along. That price doesn't count for the trailer. I'd add $400 for the trailer.
With you being experienced with the repair of the standard 2-cycle engine, can you localize the knock? Does it sound like it may be a connecting rod? The compression you've given is within good operating range so it's kinda hard to tell without actually being there. I might take a plug out, turn the piston up TDC and see if I can see any dings in the top, like something got into the combustion end........other than that, it's anybodys guess. If you can pop off the head and look into the cylinders to look at the pistons and sleeves to look for damage. If you do and you don't find any, then it's gonna be in the lower end...
If the ski is in excellent condition outside the knock, I'd probably want it and just do an engine replacement. Remember, if you do, you have to provide a rebuildable core to get a good price......