Just found this thread.
Flood bike possibility....Don't start it. You'll just waste any good part left in it.
Been there before, a few times.
Flood mud, fine silt, does not rinse off. If you even suspect it, tear it down and clean each piece thoroughly, then do it again. ( parts cleaning tank of some sort and air compressor needed)
The fine silt will adhere to every surface, load up in every machined pocket and passage in the head ,oil journals, pump, load up rings,bearings, and get into every moving part. Every part needs a thorough cleaning individually.
Of course the transmission is the same way and will destroy your work should you decide to only clean the head and piston topically. Since engine and trans share the same oil pool , the tranny will infect the engine...cases must be split, all pieces removed, all surfaces thoroughly cleaned...every piece washed and blown individually, twice. There's no working short cuts for clean, it takes time to do it well. If you fail at clean , your bike will fail....every part individually twice. Or you are just wasting your time,energy, money and ruining the possibility of ending up with a completed ,dependable machine.
This is your chance to learn everything you ever wanted to know about the 550, your chance to break it down , clean it out , replace what's needed, put it all back together. You can do it, don't be scared. Tons of help here, good people here who know how to help. Do it right, and be proud to ride it.