So my F is now naked and I relocated a bunch of wires and put electrical type around most of them. I went for a ride this morning and all was well. It rained for a few hours here in FL and after it stopped I went to go for a spin and the bike will turn on but will hardly idle. With full choke it is reving to about 1000rpm max. Anyone have any idea what could be happening? Do I need to make sure one item in particular is covered from the rain? I'm hoping this issue is just electrical and when it dries all will be back to normal. Any input is appreciated. Thanks.

hey bud i would go through and redo an connections you did with regular butt connectors and change them out for heat shrink water proof connectors and then electrical tape everything back up.  That will insure that your not getting water in any of your connections.

Yeah I need to cover wires better... So since it was idling so low with full choke I started to think it was only running on one cylinder. I pulled the left plug and it still ran without a change in Rpm... pulled right and it shut off, so this is my problem then right? I was also thinking I heard a clanking noise in the engine, may just be my mind playing tricks on me. What could have happened here folks / how do I fix it

may have fouled your plugs.  i would swap out for a new set

plugs are brand new...

Check the fundamentals. Fuel, air, spark.

If you yank the spark plug out of the engine and ground the outside of the plug to the engine, do you have spark, or not?

If no spark, follow that (swap plugs does the problem follow the plug, or stay on the original side? Then - swap coils - does the problem follow the coil, or does the problem stay on the original side, etc).

If you have spark, look for fuel supply/carb problems (use the carb drains and see what comes out, etc) - smell the plug and see if it smells like gas, or looks wet. If your tank filler rain drain is not working right, perhaps you pulled a big slug of water into your carbs, and it ran more (sidestand?) to the left side...

Most of the connectors on the bike would not really expect to see a dry environment - a fairing is not much cover, so most are made to resist water to some extent. However, if you've relocated and replugged a lot of stuff, something might simply have come loose or been poorly connected - or turned upside down so it does not drain water correctly...

I was planning on swapping the plugs tomorrow to see if it followed the plug or not, I will also ground the plug to make sure I have a spark but the plugs are brand new but who knows could be fouled.. what exactly is the rain drain? Is that the long tube at the bottom of the tank? Thanks for the help Dod#i I'll post again after I do that... any more ideas?

The rain drain is the tube that starts under the filler cap (beside the fuel-filler opening) and out the bottom of the tank - after which it should connect to a hose that comes out by the right footpeg, along with at least two other hoses (airbox drain, with the funky slit cap on it and battery vent).

So I went to pull the  plugs and before I did I started her up only to see that both cylinders were running again leading me to believe that this has something to do with the rain yesterday for sure now. It was still running poor but it was a start. I pulled the air filter and sprayed some carb cleaner into the carb but it doesnt seem to be helping... should I just pull the carbs reset float height and clean everything out? The bike mostly sat for almost 2 years leaning on its left side aka where the bad cylinder is.