I took my F3 for her first "long" ride a few days ago. It was a 40 mile round trip to a buddy's house and back. About 15 minutes after doing a steady 50-65 MPH, I hit a busy intersection with a traffic light and went through a period of 10 minutes of stop and go cycles. My bike started sputtering and it became necessary to have the throttle cracked to keep it running. I also had to open the throttle 75% or so to get it started again. On my way back home as soon as I hit open road and she cooled off from midway on the gauge, the bike idled perfectly again.

I also noticed something hot under my right leg which ended up being my R/R. My F3 is naked for now. Does the lack of proper ducting cause hotter temps?

 

No, the cooling on honda R/R's is terrible and they overheat. Sounds like your bike is overheating though. Does the fan kick in? How high did the gauge get? When my bike gets hot (about 2/3 up the gauge) the fan kicks in, but you feel a hell of a lot of warmth on your legs. The fact you needed to gas her to get it to go doesn't relate to the R/R.

 

It never went above middle on the gauge. No bubbling through the radiator pipes indicating boiling. I don't believe the bike was overheating and I also don't think my fan kicked on. I like the hard wiring the fan idea and ill definitely try that out.

 

Can anyone else think of anything?

 

Visually inspect the r/r. Is the epoxy-fill cracked or bubbly? Check the connector to it.
Is it showing any sign of heat damage, ie warped/melted and or burnt pins?

If so, it will need replacement. Whether that fixes your problem, maybe.
However, if you see any of the above symptoms, it is contributing to them
and should be addressed.

Hope this helps, Ern