I have a 4115 with the 47 snowblower, I think your tractor replaced mine, anyways, my pto shaft is also at an extreme angle to clear the pumpkin on the front axel. I had a issue with the two bearings that the pto slides thru, in the mounting brackets on the front of the tractor. Mine loosened, each bearing has 3 bolts (I call them a flange bearing, not sure what JD calls them), anyways if you loosen them, you will find that thel also adjust up/dow and right/left a little, mine had loosened, and allowed one of the universal joints to just hit (tick) on the from axel housing, which could be seen on the axel and the pto shaft. If you do loosen them, before you tighten them, insert your pto shaft thru both and tighten, or you could have an alignment issue thru the 2 bearings. You might want to have JD dissasemble thse bearing, they may have not gotten lubed at the factory and have gotten noisey. Just a thot, hope you find the problem!
Bill