This is a lot of substrate. Setup is typically 1" dirt and 1" gravel cap. With sand cap, even less. On a larger tank like this you can get away with slightly more than this, but it still seems like a lot. I'm not sure about the pH (maybe anaerobic conditions raise pH?) but I agree with @johnwesley0 that your substrate is likely going anaerobic, causing your plants to grow poorly.I've got almost 1.5" of organic garden soil, then almost 2" of black sand (the inert Petco sand).
Poke the substrate as johnwesley0 suggested and see if you can scoop some of the sand out (or maybe vacuum it out) to lower the cap. If you notice black slimy roots on your plants that smell bad that is definitely an indication that the substrate is going anaerobic.