Does this tractor have a fuel pump in the tank to feed the injector pump?  If so, that pump could be the culprit.  Either by not pumping, or it may have a bad check valve which allows the fuel to drain back into the tank at night.  Once the fuel is pumped to the main pump during extended cranking, it would run fine.  I suggest that you also look for leaks near the tank, like lines rubbing on the frame, etc.  It may only be a pinhole, but allow the primary filter to empty overnight.

You should also check if your tank is a plastic one, I had one like that that used to produce a sediment  that would clog the filters. Wish it would be usefull.
Regards

At the fuel outlet from the tank there is a tap to stop fuel when doing repairs to the fuel lines. Remove the fuel from the tank then remove the tap and check if it is cloged. I once had a similer problem to yours and this was the culprit.