I thought I was an ok mechanic untill.....

Alright I'm back. I haven't touch the bike since june. I haven't ridden anything. There has been no motorcycle related thoughts in my head. Untill....
Yes I did it, I looked under the tarp and saw my bike there. Now I'm going to be going threw it from the spark plugs out. Hopefully testing the components I have to make on a good running bike to make sure they are good before I replace them. But I will replace whatever is required. Once I get spark I'll rebuild the carbs, then all the maintenance issues that pop up on these olds yamahas. I had almost had my xs done when I decided to take a little break from bikes and will probably have that on the road with a little luck (waiting for a gas tank to pop up). So there you have it, I'm back and ready to kick this bikes ass. I need to thank you all for your patience and can't wait to get this thing done.

 

Quick question for the gurus. If one spark plug is not grounded will the other plug on that coil still fire? I know it seems like a dumb question but I remember working on an old chevy that was like that.

 

With waste spark coils - coils that connect to two plugs - both plugs will fire at the same time. One will be igniting on the compression stroke, the other will be sparking harmlessly on the exhaust stoke. If one plug isn't connected, the other on the coil won't work. They form a circuit, you see.

Your problem sounds like pickups or wiring.
Make sure the gap between the reluctor and the pickup is at spec... I don't know what it is, but there's a spec out there.
Testing a magnetic pickup is pretty easy. Connect something that'll give you 'movement', be it an analog needle sweep, or a bar graph on a DMM, or a waveform on an oscilloscope...
Again, I am not sure what the spec is, but there should be an equal amount of 'movement' on both pickups.

For wiring, tear out every wire and connector, and closely examine them all. Replace every wire and connector if you have to. I'm thinking about doing it on my bike - replace those corroded bullet-style connectors with something a little more weather resistant.

 

Bobcharles, you've got it. I plan to make a whole new harness if I have to.