Two possibilities. 1 is that the oil is frothing and you are checking it whne it is full of air. This would be more likely on a hydraulic equipped tractor, and being checked right after use. 2 is that it is indeed water, and you are correct that the shifter boot is the source. Check the fluid after the tractor sits overnight. Carefully loosen the plug and seeif water flows out first (I once took a quart of water out of the trans). Then check the fluid. If it is still cream colored water is the culprit. If no water and the fluid is oil again you pump may be frothing it. If it;s water try the following. If it doesn't have a hydraulic pump, on a dry warm day, drain it and fill it kerosene, drive around for a couple of minutes early in the morning, then drain and leave the fill and drain plugs out until the evening. Pull the shifter boot off and replace it. Put the plugs in late in the afternoon and refill.
If it has hydraulics, pull the plugs and boot, compress the ram, but do not put kerosene in it. Let stand all day, refill, be sure to cycle the hydraulics, then let sit over night check the fluid, and repeat as required. It took 3 flushings to get mine cleaned out. Or you could disassemble it totally and clean. Pain in the butt.
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