Hmmm...read a bit more. I think adding Prime (which I can't remember if I suggested it) might not have helped if you're tank is still cycling. With your tank being young and possibly still creating it's bio-filter, the Prime would bind things needed to "complete" and maturate your bio-filter. Basically, the ammonia isn't a bad thing in a young tank that is cycling. It is necessary to make nitrite which is then turned to nitrate. So you're nitrate "spikes" could very well be coming from the process of ammonia being converted since it is still present.
I don't think your sand bed is "dying". I personally don't think flow has anything to do with the ammonia or nitrates. Many people run deep sand beds (DSB's), like I do in my refugium. In those scenarios, flow is severely limited over those sand beds but they are phenomenal at creating bio-filtration. Granted, DSB's need to be deep as is in the name, for this to work properly for the intended purpose...but just mentioned to say that because there is a dead spot in flow doesn't mean that part of your sand bed is dying.
BESIDES...the large majority of bio-filtration comes from live rock. Porous live rock harbors the largest surface area and ability to colonize the bacteria we all need in our tanks. This is why many people have bare-bottom tanks. Sand is not a requirement for bio-filtration. Most FOWLR tanks that have fake coral inside, require a good sized bio-ball system to create it's bio-filter.
This brings me full circle to the fact that I think the ammonia present in your tank is slowly, but surely being converted ultimately to nitrates which is why you see that rise. I would let the cycle complete to get that ammonia out before dosing anything else or trying to "clean" up your water. It's trying to balance out in my opinion and with so much intervention it probably is having a hard time.
All IMHO of course...