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Could be a coil. They loose efficiency when they get hot and get crummy with age. Other people have had similar problems and their coils were at fault. Check the battery wires too. Mine runs real lousy when the cables are loose, but it starts hard too when that happens.
Factory set-up is very lean. Weather gets cooler and they balk all over the place before they are warm. You never did say what mods you had if any. If none...
Drill out the EPA plug on the bottom of the carb and open the low speed mixture screw 1/2 a turn or so.
You can find very good instructions for carb tuning at nightrider.com.
I've already done a stage 1 on my carb from here: http://www.harley-performance.com/ . I backed out my mixture maybe a quarter or so the other day. Could that just not been enough?
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