Going to pull the valves this weekend and clean them but what is the best way to clean the slots they go into? Do I need to worry about crud going into the cylinders or will it be fine when I fire it up?
You could try moving the piston on the cylinder you are cleaning into a position where the side of piston will be visible (top dead center) so that it will block things from falling into the bore while cleaning, then use a vacuum to suck the debris out.
A thin file wrapped in a rag soaked in carb cleaner worked well for me