You can buff the piston heads with a power wire brush. Don't get real agressive, you can scar the heads. If it doesn't come off with the brush try the scraper. If it still doesn't come off bung the piston back in the engine. If you can't get it off it won't come off in the engine.

In my experience with gas engines the cyp. head bolts can be reused. On my Diesel trucks they can be reused once. Cyl. head bolts do not have to go back into the same holes from which they came.

As for as cleaning the bolt holes you should take the block to an engine rebuilder and get them to clean it in their tank. Most modern shops have a machine that sprays the block with a very hot caustic solution. Remove all aluminum parts or the caustic will do it for you. The engine will come out much cleaner than you can get it and it will probably only cost you $20 or so.

Definately tap all the bolt holes, not just the cyl. head ones. Be careful when you blow the gunk out of the bolt holes. It comes out straight back into your face a lot faster than you can move out of the way. I understand that there are very few jobs for blind mechanics.

Thread lubrication is a much debated subject. Some people use ATF, some Never-Seze, some STP, and some just clean the bolt and hole and use no lube. Check with the local MB shop. I know that there are different torque tables for lubricated bolts than there are for dry ones. I think that clean, dry threads is the way to go.

When I started building engines in the late 50's we used to have to soak head gaskets in the bath tub overnight so they would expand and seal correctly. From what I have read in the gasket sets I use lately all gaskets go on dry. Again, check the manufacturer's recommendations. There is often a note in the gasket set that will tell you what to do.

If your heads are in the machine shop you might ask them to Magna-Flux them to check for hairline cracks.

I hope you have an engine stand on which to mount the engine before you start re-assembly. They are dead cheap at Harbor Freight and worth their weight.

Good luch