Flyin' by the seat of my britches, here - with all that you have said, I think I'd be looking real hard at the cylinders, pistons, and rings for fit, clearances, and roundness of the bores and pistons, or perhaps just one of them (?). Mic everything really well, double check end gaps and gap alignment, and only use oil on the cylinder walls and rings on assembly; the grease might not hurt anything, but, on the other hand, it might cause a problem. If you are going to store the engine, squirt some oil into the upper cylinders after you are done running it, and turn it over a couple of times real easy by hand to spread the oil around, and put the plugs back in and seal it up; it should be fine.