I don't have the same exact problem, but I'm going through the same dilema. I even bought all new substrate over the weekend and was ready to do a complete changeout, but at the last moment decided not to. My tank has been set up over a year also. I'm sick of the mess my 4 inches of sand give me. The fish constantly blow it around at night, getting all the LR looking like it snowed out and leaving big caves under everything. The detrius that collects, the algae at times, although I found out a few causes of this; topping off with tap water - phosphates, low salinity - red slime algae, overfeeding - detrius, etc... So... I'm looking at my tank again last night and have decided to do this. I am going to gut the tank, trying to save as much "live" stuff in the sand, snails, crabs, feather dusters, etc... I then will take all my LR and put them in 15 gal tupperware containers filled with my tanks water, another with fish. Clean the front glass only with a razor and towel. Fill the tank with a 1 inch or lower of aggregate, and refill with 1/2 new water and 1/2 old water.
Let us know what you decide to do.