You had coolant "flood" your exhaust manifold? I'm trying to figure out a path for that to happen and can't come up with anything but a crack in the head between the coolant jacket and an exhaust runner. Take off the exhaust manifold, if that's what happened you'll see one runner is much cleaner than the others.
A service manual will tell you the torque specs and probably be useful for reassembly. Honestly I would wait to order parts until you've got it completely apart. You never know what you're going to break or find is broken once you get it apart. At a minimum you'll need the flange, it's gasket, the head, intake, and exhaust gaskets (be sure you get all of the ones you need for the exhaust).
There may be one or more shims between the head and block. These lower the compression ratio. They're all the same thickness and can be reused if you didn't damage them on disassembly. If you did just count how many there are (be careful they can stick together or to the deck or block really easily) and order that many new ones. The head gasket goes above or below the shim(s), I can't remember which, you'll see when you remove it. You can just unscrew the nuts where each fitting goes into the injectors and pump nozzles and remove the pipes. It's all compression fittings so no gaskets to replace that way. If you need to get the injectors out you can remove the assemblies as one piece, just grab the nut closest to the head when removing. The only part of the valve train that has to come out is the push rods and rocker train. Mark the push rods and head bolts so they go back where they came from.