I noticed that no one has mentioned the bearings. I have had to replace the bearings in the PTO on my 96 Craftsman. The bearings get rusted from the moisture and tend to seize on the shaft. I wonder if the bearings are semi-seized on the shaft and release after a period of run time. The best thing to do is remove the PTO and check it out. This has been a problem on my tractor. The first PTO was completely distroyed. The second PTO is checked from time to time and I replace the bearings as necessary. I got a little extra use out of a set by drilling into the bearing seal (very small holes) two in all and forcing in grease with a needle grease fitting on the grease gun. You pump in one hole until the grease comes out the other.
This may or may not be the problem, but it's worth a check.
This may or may not be the problem, but it's worth a check.