You only need to check the over-fire draft for the initial setup of the baro and stoker air adjustment. I would monitor the draft routinely from the flue pipe between the boiler and the baro...right after the boiler is best.
I wouldn't feel good about drilling that cast iron door either. Can you cut a piece of steel and drill a hole in it? All you need to do is get the boiler up to temperature and hold the cover plate over the door opening to get a draft reading. In the absence of any other recommendation, I'd set the baro on -0.05", set the air at 1/2 open, and see what you get at the firedoor.
Matt Direnzo would be a good person to ask for advice on this, he is no stranger to Yellow Flame boilers: YELLOW FLAME