Here's
the remedy for STAINLESS STEEL headers that turn BROWN : it's called Optiglanz Edelstahlreiniger, a chemical that cleans your brownish pipes in a couple of minutes.
I used it on my first R12GS with stainless steel headers (my current R12GS has chrome headers). It works a treat. Though bio-degradable, it's a bit aggressive, so instead of spraying it on (and inadvertently hitting engine parts), I sprayed it on tissues from a kitchen roll and then rubbed the headers with the drenched tissues. If you go this way, use rubber gloves. Let it work for a couple of minutes, then hose down with water (preferably not on your best tiles).
Believe me, you won't find anything better. Here are my first R12GS's pipes at 40000km after treatment :
(There's no need to dismantle the headers, I did this for a different reason).
The only downside : the pipes will turn brown again, of course.
Here's a source :
http://www.wunderlich.de/frame.php?prodid=3024570&groupid=3901
But it can be bought at Hein Gericke too.
Or do a search on the web for Optiglanz Edelstahlreiniger.
Warning : this product can't be used on chrome pipes (the ones that turn blue-ish). For the hard of hearing : DO NOT USE THIS ON CHROME PIPES.
The solution for CHROME pipes is simple chrome polish, and a lot of elbow grease. The advantage of chrome pipes is that only the front part of the pipes turn into a different colour, and you're never riding around with rust-like pipes.
I have no commercial interest in named products.