There is no way I know of to get rid of the discoloration on the stock header pipe. I tried Simichrome polish, it was removing the chrome (yes the chrome is that bad) Aside from having it rechromed (expensive) or wrapping it, you just have to live with the discoloration. I don't mind it at all on the header pipe, reminds me of my old Triumph. I don't like the brown circle on the "silencer", but hopefully I will have a different silencer soon.
Newer Harley mufflers are just as quiet as anything else anymore. Even their Screamin Eagle pipes are now street legal. Damned EPA. Fortunately you can get aftermarket pipes for Harleys. I'm wondering if there is a louder than stock slip on Sportster muffler available. I like the EFI pipe, but it does not seem to hold up very well. A Sportster muffler should last much longer, and still doesn't look out of place on the Enfield.