Time for a scrub

[outtafocus]

I have a bad green hair algea problem. This stuff is covering my glass but my live rock has very little.

My plan is to pull out all rock and scrub what hair algea there is on it, off.

I am also going to be reaquascaping the tank as I have decided I have way too much live rock for my needs. (note, I will have a few nice pieces of Figi coming up for sale soon)
What is the best way to go about his major task without causing a system crash?
I was going to drain much of the water into a few rubbermaid tubs and placing the rock into these, them just use a brand new nail type scrubbing brush to remove the unwanted aglea.

I plan on using about 50% newly mixed water for the refill, is this a bad idea?

Any advice would be appreciated.