1) Yes the head will come off with the engine in the bike.
2&3) You can do the seals one at a time, but why? It is possibe to replace the seals with the head in place, if you charge the cylinder with compressed air to hold the valves closed, and have a way to compress the springs to remove the keepers. If I remember correctly, the factory spring compressor made that possible. If you are removing the head, I would replace all intake and exhaust seals, and lap the valve/seat contact area. That way you can inspect everything.
4) Start with the engine on tdc on cylinder 1, with the valves on overlap, like you would do to change a shim bucket. Zip tie the chain to the sprockets before you remove them. Once you get the head back on, reinstall the cams in the same position you found them, using the 19mm hex flats on the cams to manipulate them enough to get the sprockets located.
5) You will need the head gasket, coolant, and valve seals for sure. I would think about replacing the valve and crank cover gaskets, since you will be removing the timing cover. You will need sealer for the cover, and you should consider replacing the seal behind the hall sensor, since you will be disturbing it. This seal is tricky to install without the factory seal installer, and that might be expensive. Get exhaust gaskets as well. Depending on your milage, this would be a great time to replace your timing chain and rails, although it would make realigning everything on reassembly more difficult for you.