Getting a proper tune will certainly lower your running temps.

 

What help are you asking for? Sounds like, "the guys" at the HD shop told you what's what. Any way, while using premium gas and changing your fluids on a regular basis is a good idea, as you can see it won't impress your right side muffler very much.

Find a reputable tuner and spend the $$$.

 

Did you at least get a "download" when the pipe and filter were put on? If you're running stock OEM tune, which is already on the lean side for EPA, with slip ons and AC, then you are running super lean and should be happy that's the only discoloring, and hopefully only problem as a whole, that you have.
You probably have some nice dark blue headers to go along with them.......... As stated if you haven't already get a tune or a tuner and program it yourself.

 

Putting it in a "nicer" way, your bike's definitely running hot/lean and even though the pipe's discolored, it's fine (other than discolored outer chrome). Definitely get a tuner...cheap one is Dobeck TFI (easy too). Also, if you're detail oriented (like me), you can have the pipes re-chromed, or ceramic coated to freshen up. Enjoy!

 

looks like the wrap on the baffle has blown off ...pull the baffle out and you will see where it has been blown off ...that's where the heat is hitting the chrome ...compare with the left side ...