IMO taking the rock and/or the sand out and washing it would be more harm than good. It would inject new die off into the tank and also wipe out whatever natural filtration you currently have. In the short-term I would be skimming wet and keep up what your doing (except I would tone back the 50% water changes as the fish need stability and large water changes don't provide that). Long-term, you can set up a refugium with macro, run a reactor with bio-pellets or some other media designed to reduce nitrates.