I would be very skeptical about the fuel injection timing changing by itself. Was the tractor motor running when you got it? Has the injector pump been removed/changed? You say you notice that the fuel is being delivered at TDC. I guess I wouldn't automatically assume there is a problem based on this observation alone. If it were me, I would finish swapping parts and then start it up. If it starts and runs fine, the timing is probably good. If it doesn't start or run good, then I would start my further troubleshooting.
By the way, how much did you get the tractor motor for?
1983 Fraser 41
La Conner, WA
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Boating for over 25 years, some of them successfully.