Also, on my way home just now I blew my main fuse. Thank god I already got up the hill right by my house. stock harness and wiring, Dave?
Battery is charged up to 13.91 volts. so that's a tad high  
Headlight is still going out! Is my ground not good enough? I don't smell any burning wires but after about a two hour ride my buddy looks back and sees that it's out. Any ideas for me to check?
Of course, start with the fuse itself. Is it the correct Amperage? Is your wiring stock? What is the Wattage rating of that unit (curiosity only?)
Stock wiring harness but with modifications. I rewired the back half of the bike when I was making the battery box under the seat. Stock colors and new connectors from CycleTerminal.com
I'm also using a Shorai LFX14A2. Is 13.91v a little high? From Shawn at Shorai: 
"Please verify the charging system output measures 13.6-14.4V at the battery when the engine is running at a high idle (~2000rpm).   The charging system should not drop below 13.1V or above 15.2V at any rpm."Now, my battery did just go to about 7 volts last week when I was trying to time the sh*t Daiichi points. I charged it back up full and it didn't seem like it was damaged, could be wrong though. But I've been having the bulb blowing problem for the last few weeks. 
Yup, correct fuse (15amp). What's the wattage rating of the unit? You mean the bulb? It's a 55/60 watt H4. 
I've been considering one of the Cognitomoto 20/30 watt LED bulbs for less of a draw.