I finished up one side. I used the stock nut and washer on the outside but used my bushing and flange on the inside. Those parts run true enough that I was able to determine that the crazy run out is actually in the wheels. I just put it all back together and honed the wheels as true as I could get them to a useable (non walking across the bench) state... I took a lot of meat off but they run okay. this will do for now.
On a side note, I have been considering a silicone carbide wheel for the few carbide tools I have been using. The aluminum oxide wheels obviously don't touch them, but the dressing wet stone I have does do a bit, but not very much. I have one tool I can't use cause it has a chip. Would be nice to grind back to a point.
Anyone with any experience want to chime in and tell me if it's worth buying?