Have you looked up in the hole where the shaft goes in? Maybe something in there , a chip of metal or something? Also be sure the 540 shaft has a bearing race on the end of it. It should be a press fit on the end of the shaft, but sometimes I have seen them come off and stay up in the tractor when you pull out the shaft. That would keep the 1000 shaft from going in also. If it did come off, reach in there with a magnet or piece of wire with a hook on it to pull it out. You can then slide it back on the 540 shaft and tack weld it on. Don't put it in the storage position without making sure it is secure on the shaft. It could fall off an get into the gears causing damage.
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