I wouldn't be concerned about all the stuff floating around. You wanted the LR
to cycle your tank and it is going to. Remove whatever is floating around....but just be patient...things will clear up.
Scrubbing that rock is only going to injure or kill other things that may still be alive.
At some point, the rock might start to even look moldy...again, that's the cycle and it will pass.
Hang in there.