It is what it is!
This is another case of a basically full size implement on a less than full size tractor. The only real solution if more clearance is absolutely necessary for that implement is a shorter auger.
Here's why:
1. The arch yoke, for maximum lift, should be adjusted so that it is as near 90 degrees to the lower three point lift arms in the raised position as possible. In the side view pictures it's pretty close. Bulldog is right that a taller arch will increase lift, but it causes another issue for you. More on that in a second.
2. Using the lower hole of the three for the top link (on the tractor) will increase the mechanical advantage of the three point system (in relationship to implement tail end lift height). You've already done that. Moving it to a higher hole will have the effect of lowering the tail end of the implement UNLESS it results in a more square relationship of the arch yoke to the lower three point arms. Even then it may just be a trade-off.
3. Finally, you're probably already exceeding the maximum operating angle for your power shaft. Any arrangement that further increases lift will also increase the angle of the PTO shaft yokes and would likely result in damage, or at least severe vibration. I'd be surprised if it didn't already shake a little in the raised position, and I'll bet when you have it all the way up your safety cover already rubs on the adjoining yoke, doesn't it (it's not really supposed to do that).
I think you've done all you can do for that auger length. Only thing left is to maybe let some air out of the front tires on the tractor.
