OK, first run a fuel that is all synthetic. The brown spots are from the castor oil, and if the fuel has any in it the brown spots will come back.
Now, the way I have removed it, before I started using Wildcat exclusively

Was to use some rubbing compund to get the brown off, the I used some automativew wheel polish for aluminum wheels. American Racing makes a great product that will make your muffler look like a mirror. Its a purple colored liquid that you just rub on and polish it as far as you like, then buff out with a clean rag and whew does it shine.
The hardest part is getting that crappy castor oil burnt stuff off. It is hard as a brick, and most any other abrasive will scratch the muffler surface pretty good. I have heard of others baking it in an oven in a solution of some sort. I am sure someone else can answer that.
For now the rubbing compound will do the trick, it just take some work to get it all off. Remember, full synthetic, and it will never come back.