Rec/Reg has alot to do with the start, more than you think.
If your battery doesn't have the balls to turn the engine over fast enough, fire the coils, run the lights as well as run the ignition system, it's not going to fire over easily. It's the first casualty when your RR takes a dump.
When mine went out, restarts were the absolute worst. I had to push start the bike sometimes to get it going after I got gas. After awhile, even leaving the bike on the charger overnight wasn't enough and I had to spring for a new battery when it was only a year and a half old. Things got expensive quick, not to mention the uneven voltage spikes may cook your CDI as well.
You're running without the air filter? On a fresh motor? That's a dumb idea, hope you haven't run it so much as you're just doing more damage than anything.
Better get it together or else that bike isn't going to last so long.