Xfaxman, thanks for that input, that's kind of what I was after. How would one check for this? I don't have a quick hitch, and if anything I was tending to operate the cutter more with the tail end raised than drooping. I suppose that operating at near the minimum overlap (approximately 6 1/2") that with a replacement shaft I should be looking to have a greater overlap (ensuring, of course, that it's not fully collapsed when the top link is at its shortest).
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The more I think about this the more I'm almost positive that the shaft was bent when I bought this thing. The reason I suspect this is because the U-joint (tractor side) had one (or two) of the cups showing cracks (might even has been a small chunk missing) on the cup edges. Seems that a bent shaft would put a lot of stress on the U-joints.