Switching to raw is a good option. You can't get any more 100% natural than that. It's easier to digest too so the body won't have to work so hard to process it and his liver won't have to deal with extra stuff.
I really would like to see test results tho. There was something in your update that didn't sit right with me and I couldn't figure it out until now. You said all you did was hand them a urine sample. Yet from that one sample he was able to determine high phosphorous and magnesium levels?
Before I suggest anything else we have to determine for sure which type of crystals they are, that is super important before deciding what to do.