I do believe it to be running Too LEAN...
Cold weather temperatures will SHOW Lean Problems....
If you Don't have a fueler installed and the bike has exhaust and air cleaner changed to allow better breathing, (Stage one),,, You Need a TFI of a Gen3 to increase a little fuel to UN-LEAN the bike...
There are other fuelers out there but the Dobecks TFI or Gen3 will do a great job and the price is right.. Dobecks gives our members a 50$ discount and free shipping.... Can't beat that...
I run a carb 06 sport R 1200 and do understand what I say when I think You have a LEAN condition and running too low in the RPM range MAY be IT and along with a lean condition..
Like glider mentioned.. SHIFT Down a gear or even Two to see IF that Helps out... Idling a motor in third gear Will cause the condition you are having.. Make sure it is revving enough to FEEL good when you twist the throttle and not popping or sluggish...
If not,,,,, you are also probably too lean... A Hick-up means too lean and usually shows up in Cold temperatures...
Also you say it was JUST modified to a stage one??? Stage One NEEDS more fuel to make up for the lesser fuel by opening up the air/exhaust on your bike..
When it was Stock on the air and exhaust, it probably was still too lean BUT,,, Did it run good???...
If it ran good before the conversion, IT Has to be Too Lean Now...
Right off the show room floor,,,HD has to play ball with the EPA and that = TOO LEAN...
signed....BUBBIE