Well, first piece of advice is that you shouldn't do it with the engine in the car.
Honing a block requires honing
oil, and there will be lots of metal floating around. You will never be able to do it one at a time and keep everything clean.
Go ahead and pull the engine, strip it down, have the block professionally honed (a bottle hone on a drill will never give you a really nice finish for a modern ring seal, plus you'll never keep the cylinders straight like that), machined, hot tanked, then begin assembly.