Cleaning the engine innerds

I'm prepping the block to throw the heads back on. Had some gasket debris and other sanding "stuff" in the cylinders sitting on top of the piston so I vacuumed each cylinder last night. I was wondering about any micro grit that stuck itself to the cylinder walls or might be nestled down at the piston rings. Any good way to ensure I have it all out? And should I recoat the piston walls with 15W40 or some other suitable lubricant? Guess I'm a little nervous about scoring the cylinder walls.

I stuffed rags into the upper openings of the block but I know stuff fell in the bolt holes when sanding/scraping. Should I be concerned about this?

I'd just give each cylinder a good blast with compressed air, and make sure to check the coolant passages for debris too. As far as lubing the cylinder walls, maybe a coat of 15W40 or assembly lube, followed by rotating the engine to give everything a light coat then wiping off the excess - you don't want it getting squished on the compression stroke. Or, you can use a drill with a cheap 1/4" drive extension & 5/16" socket to prime the system before cranking.