Prepping heads/deck for in-car reassembly

In an earlier post I mentioned that I'm going to pull the intake and heads off the 289 to port and polish them this winter. What is the best way to remove old head gasket from the block deck, and how "clean" does it need to be? Does the entire surface need to be bare metal, or will a scraper and scotch-brite treatment suffice?

What method do you use for cleaning/prepping, and how do you keep too much crap from getting into the lifter valley and cylinders other than just throwing a rag over the top of them? I thought about using masking tape to the cylinder walls, with some plastic wrap or newspaper, to keep it from getting between the cylinder and bore, is that overkill?

Also, is using RTV/Silicone for the intake a bad idea when the temperature is right around freezing? No heated shop/garage, and my friend's place is occupied.

It cant be too clean. You must remove all old gasket. I use razor blades and a dye grinder with a plastic bristle disc. I cover valley with clean rags then pour atf over the valley to rinse the loose debris into the pan. Always change oil and filter before starting. Pay close attention to the had places to get to like around the alignment dowels.

If the heads haven't been on for a long time, they should clean up with a rag and solvent. I too use the razor blade. Do you have a shop vac, if so, use it while you are cleaning.
I've used that method many times and it works.

Scrub the CRAP out of the decks. They need to be so clean you'd eat breakfast off them. Use whatever - I like lots of WD-40 and a scotchbrite pad on a piece of 2x4. I then follow with trans fluid and fresh scotchbrite. Wipe with ATF until a white cloth stays clean (well, red but not red with debris). Wipe the cylinders out too - use a shop vac and rotate the engine to get any debris out. I fill the valley with towels.

When it's time to put on the gaskets, cut a pair of long 7/16 bolts and use them as guide pins. Clean the surfaces with brake cleaner and dry with compressed air. Do not touch the sealing surfaces. Open the new gaskets and handle by the edges. Drop them straight down on the deck, then follow with the clean dry head. Add head bolts and torque in sequence to specs.

For the intake, I use RTV for the end seals and Mr Gasket Ultra Seal for the ports. I also use a pair of long 5/16" bolts for alignment pins. You can stick the gaskets to the heads with Permatex aircraft sealant, but use sparingly. The RTV end seal trick requires a bead of sufficient size to fill the gap, then wait about 10 minutes for it to get a little stiff. Then put a very thin coat of RTV on the intake and set it straight down. Hand torque the bolts snug then let the RTV set up. After a couple of hours, torque a little more. Next day, do the final torque. I prefer Permatex Ultra Black.
Permatex Application Notes

Personally I would never use a scotch-brite on an engine. I've personally seen too many issues with them. From bearing damage due to the small particles they leave to uneven surfaces caused by removing metal.
Ford put out a service bulletin to their dealerships in the late 90's forbidding their use on any engine repair.

A sharp razor blade, solvent and rags is the way to go.