I have a 1980 yamaha 650xs, it is hardtail and damn fast but latily I have been have this problem. It will only run on both cylinders if I pull the one plug boot off and hold it a quarter inch or so from the plug ( it runs great that way) but if I put it back on then it will only run on the other side and runs like crap and dies. I am not sure what to do
?

Check your spark plugs.
Back in '81, I drove from Vegas to Key Largo in 6 days on a XS 650 SG with an 85 Pound Duffel Bag. Nice Bike.
If I remember right, It has 1 coil, fires both cylinders each revolution, firing on exhaust stroke has no bad effect. I would check or change Spark Plugs. Good Luck

Thoughts:

. Replace coil, which may be breaking down under load.

. Check points, point gap, and engine timing--right cylinder is likely timed by changing the point gap; left cylinder can probably be timed using a timing light. Run timing light off a supplemental battery (car battery), not the motorcycle's battery.

Thanks guys, I am going out now to check the plugs I will let you know what the outcome is. Thanks again.

All right I pulled the plugs and it was very fouled, replaced with new one and it runs great. I had just replaced the plugs a few months ago, so why am I fouling plugs so fast? I have really put very many miles on it. They are the stock plug type , do I need to go to a hotter plug? Anyway thank you for the help, and I hope th replay the help some day if I can.

A hotter plug may help for your riding. Use Best grade oil you can get. The price is cheap for the good it does.

I use yamalube and it is a little spendy but it is worth the cost I feel. I will try the hotter plugs as I have added a after market dyna ignition and big bore this motor. Thanks for your help.