That valve spring compressor might work. It's certainly the cheapest one I've seen. You can go cheaper and pick up an 8" C-clamp from Horrible Freight and cut a window into a piece of PVC pipe or an old socket. (I used an oxygen sensor socket on my 850, but I don't know if that's too big for the 550.)
That valve shim tool is the right one.
I can't imagine how you've managed to disassemble the engine so far without an impact screwdriver!
Search the forum for threads on case sealant. There are many options, almost any will do.
As for cleaning the gears, solvent of your choice followed by compressed air should work fine. If they look clean, then they probably are. In the future, don't leave a disassembled engine hanging out uncovered in the garage.
Crank and gears should drop in to the new case, but follow the manual and measure everything, especially bearing clearances.
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