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Would an after market pipe (i.e. fmf gnarly etc) work fine with the stock silencerr or would I have to do something to mod them. Also, does anyone make a pipe the same color as the silencer and stock pipe?

most aftermarket pipes are plated. The stock silencer will work fine with any aftermarket pipe.

but i would expect you could get a can of high temp flat black paint at just about any hardware store right?

according to the sticky on mods there is no real gain in replacing the stock silencer

If you went with using a high temp paint on a plated pipe it would probably fall off pretty quick unless you sand blasted the plating off. Maybe stove polish would take the heat better than a high temp paint but I think you would still need to remove the plating.