hmmm….. weould like a better idea of how the cooling system works for that bike…I will go at it from a cars PoV.
Coolant in the upper side…. not bad…UNTIL, you fire up and get compression going, and fail to make sure the cylinder walls are relatively clean and again lubricated before putting a load on the pistons. If some coolant is left to bypass rings it will wash the lubr. off the cylinder walls and even prevent more from getting back on. Creating swelling, stick and snap process.
Did you use a torque wrench to tighten everything down? Was there any use of a thread lock before and after adjustments made. If torque wrench was used……when was the last time you had it calibrated?
As far as the nut goes….. afraid a tear down may be in the near future. Unless you have something that can get into the drain down ports for the oil, if not found in the case.
One scenario from above could have been a result in miss adjustment to where the cylinder could have actually slapped a valve causing the reaction to stress the rockers to the point of breaking.