"If that's the clearance when the tiller is raised to the full 3pt height.. you should be okay."
Actually, the pto needs to be trimmed for when they are 'exacty' parallel from each other. That will be the shortest distance. On most CUTs I believe when the 3pt is all the way up, the 2 knuckles of the pto will be the farthest apart. But this is different with all tractor/ implement combinations.
Anyhow, measure when the 2 knuckles are on a level plane, as this is when they are closest together. Add an inch or so for clearence. Note that using different holes for the top link (if your tractor has more than one top-link hole) can drasticly change things, as well as different top link settings (screwed in or out). Be aware of that, & perhaps make a bit more room if you are not the only one hooking the implement up.....
The pto shafts should not compress to hit each other (breaks something maybe even your tractor) and should always have at least 6" of overlap when 'fully' extended at the top or bottom of the 3pt movement (or they fall aprt & make a real mess...) Anything in between is fine. Leaving them as long as practical (without hitting) lets you adapt to other tractors that might need the shafts longer. If the shaft is too short for a tractor, the only solution is a new $100+ shaft...
--->Paul