What happens when you try to extend the drive shaft further out? From what you've posted, you haven't used the PTO before, so I'm going to make a guess that you don't realize the implement drive shaft extends to suit the particular tractor.
Going on that assumption, the driveshaft is in two pieces, an inner and outer element that telescope together for adjustment. Sometimes these get "frozen" together if it hasn't been used for a while.
Each manufacturer has different specs on how much of the overall length needs to overlap for safe operation, but I'll try to give you a guideline.
Once you get the two halves moving inside one another, lower the PHD until the driveshaft would come straight out from the PTO stub shaft if it were coupled up, the gearbox should almost touch the ground. You may have to extend the digger out over a deep ditch or into a hole to get this. The idea is to establish the shortest possible driveshaft length you can expect under normal conditions.
With the shaft fully pushed TOGETHER, as short as possible, there should still be clearance between the end of the PTO stub shaft on the tractor and the end of the driveshaft coupler. This means you can't damage anything because the shaft line is too long. A good thing.
Next pull the two shaft halves apart. Begin to put them back together. As soon as the male end is just started inside the female end, take a paint marker or something similar and make a mark on the inner plastic driveshaft guard 12 inches from the point where it overlaps the outer plastic guard.
When you push the shaft further together, once it has 12 inches of engagement the mark you made will disappear inside the outer plastic driveshaft guard. This is the minimum safe amount of "mesh" you can run the digger with. The numbers vary depending on opinion, but I consider 12 inches to be safe.
Now couple the driveshaft to the PTO stub, and fully raise the 3ph. This should be the longest driveshaft position you'll encounter, and the mark you made on the inner shield should NOT be visible, in other words, you have at least 12 inches of engagement.
If you already know this, I've been mistaken and I apologize. In that case, you DO need a longer PTO shaft..
Sean