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Well John I had the same thing happen to me, I come down to taking the Bio pellets out and just do water changes every 10 days to 2 weeks, and went back to GFO and carbon my tank never look better, that is my 2 cents.
Well if you are going with a mag 5 then the outlet is half inch no need for one inch, go with half inch pvc all the way and add in your ball valve and a union so if you have any problems with pump you can disconnect real fast and fix or clean.
Mike I think you are going to need about 300 to 400 pounds of rock, I did RBU1 tank and that was a 300 gallon tank, we used about 600 pounds of rock. What a beauty when it was done.