I'm having trouble with a short, namely when I start it on occasion it cuts off entirely and the dash lights go off, then after a few mins the lights come back on. Also the headlight flickers some when it use and the speedo (not the RPM, just the left side) does not light up.

Thank you in advance.

You don't have a short. If you did, the fuse would blow.
Most likely you have a loose or corroded connector in the headlight bucket. If a newer model (2004+) then all your connectors are under the right front of the fuel tank.

Check all the connectors. Unplug then re-plug them so they wipe clean and you insure all are connected. If you have some contact cleaner, OK to spray the connectors as you reconnect them. Radio Shack or other electronics places would have contact cleaner. Probably auto stores, too.

You can trace wires on the wiring diagram. The wires are color coded so you can follow the things that have issues. Also each connector is different so you can locate a connector based on the number of wires in it and where it goes (when comparing to the color coded wiring diagram.)

That actually makes a lot of sense. I'll post the results tomorrow after I poke around.

wiring diagram: http://wiki.gstwins.com/index.php?n=Main.WiringDiagrams