Unfotunately I do not have any advice about the diaper rash...it sounds like you are doing all you can. Letting him go without a diaper at times is great so that the rash has a chance to breathe...
I do have a suggestions on the wipes so he won't be in so much pain when you have to change his diaper. Don't buy wipes at all. Instead, go to your local pharmacy store (walgreens, rite aid, etc) and buy the large packs of 4X4 gauze and saline solution. Then when you get home soak the gauze in the saline solution and ring them out until they are at the desired wetness for diaper changes. The saline is the closest chemical solution to body fluids so therefore does not sting when it contacts the sores. And don't wipe...dap as much as you can to get him clean and only wipe if you have to. Hope this helps