1 - I use a putty knife and clean everything I can. After it's as clean as you can get it lay a new large smoothe flat file on top of the block and press down with your fingertips while rubbing it back and forth along the entire surface. You are looking for any high spots whether it be a nick or the bolt holes raised around the edges. If you find any just rub them out with the file. 2 - No idea on those. I just use a regular 3/8 ratchet and tighten them up. There's no need to try and ring them off, just tight and done.
3 - I alway's use a gasket sealer on the water manifold. Pert near any type will be fine. Nothing on bolts but oil.
4 - Yes the flat goes to the rear.
5 - I never re torque the head bolts after running. You can safely add 5 or 10 to the highest number and forget retorquing. On a high compression diesel I will torque it to the highest spec and then loosen and retorque them one at a time in the proper sequence and then button it up. If you are worried about the gasket sealing use copper coat.
Premix that coolant before you put it in. There is no water pump to do it.
Make sure every hole in that gasket matches block and head before you start to put it back together.