If you paint it with spray paint.....it will hold up for a while, look somewhat funky in the process, and need to be redone frequently.  Sitting outside or riding it in the rain has a big effect on the durability of the paint.  When the paint is subject to heat cycles it gets small cracks in it....and moisture quickly starts to make it fall apart.  Any road crap, oil or bugs thrown onto the paint will permanently stain it.

Like WD says.....if you can afford a bit of time and money getting it done right....do it now.  I bookmarked this place as a promising place to send it.  $ 45 to $ 65 for a muffler, $ 14 a foot for the header.
http://boneheadperformance.com/

Maybe you can find a place to get it done locally and save some time and shipping cost...but beware not all places are equail.  A local powder coating place made some attempt to spray and bake on ceramic coating......with mixed results.  Sometimes it would hold up OK - but most times it did not.  What they found out was that we have too high of a humidity in Northern Kentucky for this process.  In the short distance from the powder gun to the header/muffler a small bit of moisture is picked up from our 80-90% humidity....and this greatly effects the durbility of the ceramic coating.  The humidity of the air has to be very low when spraying ceramic coatings.