Just running at idle will drain the battery. These bikes don't really make enough charge to put anything back into the battery until about 5K rpm. Glad to hear that your bike is running much better now.
On your #4 cylinder fouling. First, tappet clearance, from memory, which admittedly isn't as good as it used to be, it should be .002 on both exhaust and intake. Next, check the spark on that plug, pull it out and ground it to the engine case and start the bike. You should see a fat blue spark. If you have a week blue or yellow spark, pull the plug cap off, cut about 1/4 inch of the plug wire and replace the cap, making sure that it is fully seated. Last, and least likely, go looking for an exhaust leak on that cylinder, any rusted holes, exhaust clamp not seated and cinched down properly at the head, etc... In order for an exhaust leak to cause this condition it would have to be pretty severe and between the collector and the head, any holes on the collector back toward the muffler won't cause this problem on only one cylinder. Lastly, any time you remove those headers, the exhaust gaskets should be replaced.
