It shouldn't be a balancing issue if it only started after two hours of running the engine. That would have been noticed before. If it ran well at the beginning and it's vibrating now, then I guess something's loose. If the rods weren't numbered, is it possible you put some of them in ON THE WRONG SIDE OF THE ENGINE? Crank and rod-bearings only match in ONE WAY. Make a mistake here and you're guaranteed to break a bearing on at least two rods. Spun rod-bearings will losen up and shake... Grinding off just one rod bolt makes less of a weight difference than the oil you have on the crank in different places at different positions, that alone won't throw you off balance. But it might cause that bolt to fail. Having a rod only hang on one bolt will certainly shake like hell...
Any news?
Good luck, Max