I have read that valve lapping compound, as it is abrasive, should by no means get into valve guides as it will impede the reciprocal motion or damage the valve. Should I worry about small amount residue amounts that are left over in the valve shaft and can be seen through intake runners but difficult to reach? Should I try to clean it with an air pistol or water blast?
If you are hand lapping the valves you should have the springs, retainers, etc removed. You can remove the valve and clean the valve stems and guides. I would use a parts cleaning solvent on the valves. Use a nylon or plastic brush on the guides. A steel brush may scratch the inside of the guides.