First I want to thank everyone for all of the responses! It's so reassuring to see such a big response to my post and it really gives me hope that I can finally get to the bottom of this. I'll try to respond to everyone's post in the order they were posted. It's going to be long so I appologize in advance.
Victorusaconte: Your tank video was awesome. With the almond and jack fruit leaves that'll lower both hardness and pH correct? Also how long do they continue to have this effect when added to the aquarium and do they leech tannins into the water? Side note: Apistogramma are awesome, jealous lol.
SueD: Don't worry, I read your entire post, and believe it or not you may have led me much closer to my answer than you thought. It seems like you had a very similar problem to mine and now that I think about it I'm pretty sure the black sand cap that I have in my aquarium is in fact Tahitian moon sand (at least in part). I don't remember for sure if it is because it was added about a year and a half ago, but I'm almost positive it is at least in part (no pet store had enough of any one type of black sand so I believe I may have had to mix two or three different types, one of which I believe was Tahitian moon sand). I never heard of that being an issue for anyone, but then again I never checked. I did however consider changing out my substrate the only issue with that is my colony of MTS which inhabit the sand in what I imagine to be the hundreds, and I haven't thought of a good way to change the substrate while not removing any of them.
Asteroid: I wasn't aware that 15 ppm of organic nitrate is any different from 15 ppm of added nitrates (from a product like Seachem nitrogen I'm assuming?). Currently, most of my nitrates are organic as I haven't added any, but as time goes on it is slowly coming down thanks to plants, and I often don't have any species other than the snails in there producing waste, plus not much food is being added (except for the few days when I try to add fish).
Deanna: (Sorry it's so long) When I initially filled the tank I used tap water, I live in New Jersey and the water tends to be hard with a higher pH. I add Seachem Prime whenever I add tap water. I haven't used a water softener, but as you can see in the pictures there are a few moderate size pieces of driftwood in the tank (not sure how much these pieces will affect water in a 90G tho). The past few days I have been doing small less than 10% water changes using RO water instead of tap to try to soften the water and bring down the pH some (and get out any potential toxins that may be in the tap that I can't test/neutralize), it comes out super slow so the temperature in the tank remains stable at around 79-80. There is no odor coming from the aquarium. It is possible my ammonia test may be expired, but whenever I lose fish and return them to the store I bring a water sample, and every time they tell me the same readings I get with my tests at home. The only thing I've dosed since restarting the tank two months ago was a capful of Seachem Flourish (only 2/3 the recommended dosage, not sure of the ppm, sorry) and this was only once at the beginning of September (still eyeballing what my dosage amount and frequency will be depending on plant growth). Feeding I only feed flakes when there are actually fish in the tank I use Omega One Super Color flakes ( a pinch a day), I'll put in a single pellet of Omega One shrimp pellets every other day for the snails and corys, and occasionally I'll add a half tablet of Tetra Pro Plecowafers for the snails and corys as well. For my substrate, I have eco complete underneath a black sand cap. I'll skim over the sand when doing water changes if I notice a lot of waste or leaves, but there's never really any. To my knowledge, the MTS are capable of preventing phosphate pockets from forming since they're constantly stirring up the sand. The substrate has been there for over a year. Right now in the FX6 I have the foam filter pads that sit in the outside, carbon foam pads, fine filter polishing pads, water polishing pads, and ceramic rings for biological filtration. I cleaned the filter and threw away all the old media except for the ceramic two months ago when I redid everything and replaced it with new. I haven't fallen into a cleaning regime for the filter yet as it was just redone two months ago and nothing has really been in the tank aside from snails. I actually ordered a TDS meter yesterday so I should have results soon. I can't think of any environmental effects on the tank, its in my living room and our window blinds don't allow in much light. For acclimation I'll usually float 10-15 minutes then open the bag and add about 5mL of tank water to the bags every 5 minutes for another 10-20 minutes then add fish to the tank without adding bag water, I might try drip acclimation next time using a bucket over the course of an hour or two. I really like the idea about bringing the prime to the store to add to the bags, I might do this next time I purchase fish, I feel like this is something stores should start doing as a courtesy if it makes that much of a difference.
PlantedRich: I talk about at the end of Deanna's response how I currently acclimate fish, usually takes about 30-45 min so I suppose ammonia buildup is possible. I can't think of any special product I use that could get into the tank, especially since I try not to go into it too much. I have an empty 30 gallon in my basement I can fill with tap and treat with prime to use holding tank if you think that's a good idea? The only decor I have are live plants and some manzanita driftwood. I used to have dragon stone in there but I took that out months ago and restarted the tank twice. If I used the 30 gallon as a pre tank holding tank should I let it cycle or just treat it for ammonia/ chlorine with prime and heat it to the same temp as the main tank since they'll only be in there for a few hours I'm assuming? I'm also not opposed to setting it up as a bare bottom quarantine tank to house fish for a day or two before adding them to the 90 to monitor their behavior and see how they react differently once added to the 90. Thoughts?
Overall, what are the thoughts on the small water changes replacing with RO? I know my pH and kH aren't too crazy high but at this point, I'm more concerned with something in my tap being toxic to fish that I can't detect, lower pH and hardness is just a bonus. Has anyone else had issues with Tahitian moon sand as a substrate? Seems like there's a variety of things I can try not really sure where to start.