Is the stain on top of the clear? Or is the actual clear discolored? If it's on top of the clear, then try a polish and see if it will remove it. Maybe try clay? If the actual clear is stained, I'm not sure what can be done.
I had the clear on some rims with stained yellow drip marks, probably from some dressing that got left on there. Never got that stuff off, wound up living with it till I sold it.
Michael