Is there a method that will grind down the stones more than a "level"? I've been doing the sand paper method and it doesn't appear to take much of the thickness down without hours of scrubbing

Maybe some kind of file, then go back over it with a run on the sand paper?
320 paper is fine for cleaning / swarf removal, light "maintenance dressing" of stones etc. Your stones appear to be very contaminated and somewhat dished. You have to approach this just like the sharpening process of your knife it's self.
If a blade is really dull, damaged or needs re-profile....... would you start with a 800 grit stone? No you would go with what gets the job done in a reasonable period of time and progress farther & finer from there. You are trying to remove material from a stone (and contaminant’s) that is harder / hard enough to cut the steel in your knife.
Go to the hardware store and get 5-6 sheets of 60 grit (80 of they don't have 60) and 5-6 sheets of 180 grit dry paper. You can use wet and wash / rinse and have the water mess etc. it works the same just messy and more time etc. If you use the dry paper, you can just keep a garbage can handy with an old tooth brush and tap the paper against the side of the can and brush the stone when the dust starts to load. Some may argue with me but again think about it. Fast is the name of the game unless you’re bored and have nothing else to do. As you wear down the 60-80 grit, don't throw it. Set it off to the side. Follow the "x" mark pattern above when you start getting close to a uniform contact pattern across the stone. Continue until all pattern marks are gone.
Now here is where you vary things a bit. On the EP stock 120 & 220 stones, I don't do anything above the 60-80 grit paper. Just wash & scrub with a tooth brush under running water and your done. On the 320 & 600 stones, start with what you feel is need for the condition of your stone (right grit / tool for the job), in your case I would go ahead and start with a fresh 60-80 and just as the "x" marks are gone, switch to the 180 paper. When the "x" are gone and the stone is lapped flat, rinse / scrub the 320 and you’re done (your still keeping that used paper right). On the 600 & 1000 stones, finish them off with the 320 and I do recommend finishing them wet to preserve the finer finish of the stone, rinse, done.
The "used paper" can be used again and again until it’s worn out as the next progressive finer step and I keep a few cut in strips to touch up convex edges in the field. Look I sharpen a lot of knives and when deployed may use three different blades a day just depending on OP requirements. Anywhere from a very minor touch up to a chipped / chunked blade. I sharpen a lot and wear my stones as well, also some Japanese water stones I use. I had not been using diamond plates for stone maintenance until recently but I'm hooked on them now for stone lapping. I can take a semi dished 120 EP stone down to flat in 5 min. with a DMT XC 10" diamond DUO Sharp stone. I used to use SiC grit and glass on ALL MY STONES. It and sand paper work, just slower. On patrol I have used concrete hollow block, pieces of broken concrete slab and the edges of coffee cups and broken plates even!
Tip: Make sure the surface you are using is really flat and resist the temptation to move the stone in one direction to much! Rotate ends, move in a figure eight, move in a "X" pattern etc. often or you will have trouble with uneven material removal from end to end & side to side. If your going to use SiC grit or sand paper, go to hardware store or glass shop and ask them if they have any scraps of 1/4 thick glass big enough for a 12"x12" or slightly larger piece. Have them cut it and bevel it for you. I got one for free, paid $5 for the other one. It's worth it! I'll post some pic's later.
Capt. Thomas