i snooped on your reef central thread and noticed you are doing fresh water fill only with your rock is this correct? you have no salinity with your rock in the tank? if im wrong then discard this and ignore me.
just my thoughts on your difficulties are these no matter what type of tank you start there is a time frame where ph and amonia is all out of wack. but since your diy rock was in the ocean to start it up you have added fresh water only to the tank which may have destroyed all that you tried to accomplish with the rock being in the ocean. it would be like putting live rock ina fresh water dip but longer. removing all the water and refilling is really only going to cost you a huge water bill. the tankneeds to cycle it needs to get all screwed up to level out.and if ph is too high there are ways to lower it with additive.
again im not an expert nor claim to know all the answers.but maybe you shoudl start fresh. re insert your rocks in the ocean if you chose or leave theminand add some live rock toseed your rock. in the mean time fill the tank with salt water at the prefered salinity. let it cycle (you can add again additive to help boost the cycle with bacteria prodivo comes to mind). do weekly water changes and test for the spike in ammonia.. dont worry about ph just yet until the tank cycles. when you see your levels level out check for ph.
i just hate to see you struggle and by no means am i the best at this im sure ppl will dissagree with me or i missed something. and maybe im just selfish and want to see this baby running and pictures of youradditions
good luck
jeff