The most important holes will be the ones along the top where the fresh coal feeds the fire, and the idle fire burns, coal just won't burn without combustion air..
Ask Freddy to explain how to do the 'Triburner Coversion' on your stoker. Your fire keeps going out, and the coal is partially burnt
because of the Combustion fan shutting down after the fresh coal is fed to the fire.. The idle fire needs a small amount of combustion air.. The Triburner is designed to have chimney draft or direct power-vent draft pulling air through the fire, but
aparently your stove just isn't getting enough idle combustion air.. or your coal is very stubborn coal to burn at lower settings.
When you put your stoker back together, you might be able to reuse the old gaskets, but just use a thin layer of furnace cement
to seal them up.. the furnace cement is like a thin putty, it should be available at your stove store, or hardware store.
Also, since your hopper is empty, try a bag or two of different coal.. Maybe your coal needs to burn really hot, and you need a better coal for the warmer weather when the stove idles a lot..
I know this is a lot of 'maybe's' but having read through the several pages, these are the ideas I came up with..
Hope this helps.