PaulieD,
Cutting your PTO shaft so there's a couple inches overlap when the 3PH is all the way down, as already suggested, might work OK. The reason to cut the shaft, though, is to make sure it's short enough that it can't collapse fully when your tractor has it positioned at it's shortest length. I just "sneak up" on the right length, by cutting an inch at a time until I get it right.
With the tiller mounted (but not turning!), use the 3PH and top link to approach the shortest length. If you can make the shaft ends bottom out, then another inch needs to be cut off until it will not bottom out. I test the limit carefully, until the ends just barely bottom out, then use the hack saw to lop off another inch. My technique isn't the most efficient, but it works.
Then, when you test with the 3PH as low as it will go, there should be at least a couple inches overlap.
The plastic guard sleeve that covers the PTO shaft is a great guide. When you separate the halves of a new PTO shaft, each steel half will be an inch or so longer than the plastic covering it. I think the steel shafts bottom out at the same point the plastic shield bottoms out when the two halves are fitted together. Keep the length relationship between the steel and plastic and you can tell by looking at the plastic shield when you're close to fully collapsed.
OkieG