I am having a strange issue with my 99 blackbird (Fi). It runs really rough, misfires 1 or 2 cylinders for about 2 – 5 minutes in the mornings only . After few minutes it becomes to run nice and smooth. When started in the evenings when engine is cold – no problems at all, idle is fine no matter what ambient temperature and humidity is. Also twice it lost 2 cylinders after long ride in the lashing rain on the motorway …than picked up after minute or two. This looks to me like an electrical fault. Any ideas where to start looking at? I already replaced sparks (used recommend one’s for the bike, gapping was checked too), checked wiring at the coils and it looks OK. Checked ground wire connection… Something tells me fault must be located close to the engine, as it goes away after temperature pic’s up but I might be completely wrong.

Bike is stock, 52 k miles, only has heated grips connected directly to the battery and manual cct. New sparks and new battery.

Did anyone have similar problem?

Would appreciate any suggestions, thanks.