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Found one of my problems was melted wiring in the fuse holder. Installed a new fuse holder to solve this. I am trying to find where my red wire from battery transitions to white and red to the fuse, as this is the only connection I cannot see and want to check. Is this buried in the harness? 

Hi Wookie, so I got a relay and did this wiring change and now getting good voltage to my coils. Ran the bike up today and noticed a couple things. The bike has trouble when cold, the idle is low and it stalls out without throttle, once it is warm it fires up right away, idle increases and seems to cough back through the carbs much less. I also noticed that I can see air entering my fuel line backwards from the carburetors. How can this be? I checked the vent line and it is clear. Again spraying starter fluid on the boots and also the choke plunger assemblies made no difference to idle. Checked with timing light and I am bang on and the advancer seems to be moving freely. 

Air in the fuel lines is no big issue, there is an air gap above the fuel in the float chamber. Also the tank is vented so bubbles will rise through the line and exit via the the tank breather