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My neighbour is a millwright and I asked him to help me align the engine properly. He set up his dial gauges on the driveshaft and the engine adapter and found that the front of the engine needed to be raised slightly. Adding a washer under each of the front bolt holes brought the engine into alignment.
While the engine was out, I took the opportunity to install a sensor for a future oil temperature gauge.
If you're repowering your tractor, have someone who knows what he's doing help you with aligning the driveshaft.