Since you have checked the obvious,  you might try checking some less obvious things like whether your EC2 ground wires are truly are grounded.  No ground would probably appear as lack of power even though you checked the power leads - lack of ground would of course act as if you had no power to the Ec2.

 

Can't think of any other suggestions, so good luck

 

Ed A

John,

 I hope this isn't too obvious, and repetitive, but have you checked to be sure your engine is grounded? I know this is basic but is often the basic items that nail you. (Warning Anecdote follows) When working at Kawasaki in '71 they brought out the S3, a 3 cylinder 2 cycle of 400 cc displacement. It was a nice machine over all but soon they started to have misfire problems at higher RPM. Turns out it was the first time they had rubber mounted one of the engines. They were grounding only through accessories, like the shift lever, throttle cables etc... They worked when everything was new but failed as they got some wear. A small ground wire to the engine was all that it took to fix. After that I always check for a solid engine ground. Modern bonded rubber mounts often isolate the engine. I suggest a ground strap that is ok with the starter current. I ground  to the main bus or to the battery directly. If your coils are mounted on the engine that is another possible ground problem.

Bill Jepson