The mechanical filters, bio balls and crushed coral will all contribute to nitrate problems. I'd get rid of all of the above. (mech filters are OK if you clean them constantly, otherwise more trouble than good).
And yes, as said earlier using tap / well water for the water changes could easily be importing nitrate/phosphate or other things you don't want.
And yes, as said earlier using tap / well water for the water changes could easily be importing nitrate/phosphate or other things you don't want.