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rough running

I have a 01 heritage the only mods are a 2 into 1 thunder header and a stage 1 air cleaner. It also has about 13,000 miles on it. My problem is I can ride all day at 55 or 60 mph with no problems. I can also run at 70 mph for 20 or 30 miles again no problem. But when I run 70 mph for 45 min. to 1 hour I start to notice a little more vibratin in the handle bars and a slight lack of power. If I let the bike set for about 15 minutes it runs fine again. So do you guys have any idea of what could be wrong? Thanks for you help.
 
the bike was set up when i bought it. It has a stock carb. Also when I keep it below 70 it runs like a top. I also get about 38 to 43 mpg with it.
 
I didnt get a chance to check the jets but the plugs were a nice brownish tan. I changed the coil and put screaming eagle wires and platinum harley plugs in it and its running fine. best I can figure the coil was braking down from running higher revs for a longer period of time. but thanks for your help. I will keep the jet size in mind.
 
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