Check out this thread:
Loud Exhaust but only when Hot after highway run – Has me Baffled
I had a similar problem but it was worse when hot. Is the sound there all the time or is it related to how hot? I have not driven mine a lot since I tightened the air injection plugs and am thinking about replacing the muffler. The other thing it to do a good visual inspection of all the pipes. Can you record the sound and attach it?