S.O.S.

The last week or two have been rather disappointing to say the least.
After the last successful rides (which were almost two weeks ago now) I basically haven't been able to get her running again.
At first it was starting but idling only on the left cylinder. We did some tinkering with carb settings trying to be sure both were synced but, and we cleaned the air filters which were pretty nasty, and we put it all back together and then we swapped the wires for the condensers and the spark plug wires to see if that would get the right cylinder firing and tell us if the one cylinder thing was electrical or mechanical...
And now she's just dead in the water. Won't start at all. Switched everything back and still nothing.
It seems that there is spark at both points, but it seems weak at best, and weaker (to the point of maybe being intermittent) on the right. Same at the plug. Spark on both, weaker on the right.
I don't totally know what I'm looking at, but I have to say that the spark doesn't look all that healthy on the left when you get right down to it but like I say, I haven't got any real experience with it.
We've tried disconnecting different circuits to see if something was maybe shorting out and causing a drain on the power, and that hasn't helped.
Tried some new condensers, and that didn't seem to make any difference either.
The condensers and coils seem to pass the bench tests outlined in the Clymer manual, but from what I understand those aren't necessarily definitive as to whether the coil is good or not.
I guess we need to pull the air-boxes back off and see if something we did back there knocked something loose, but it doesn't seem like there was anything that much back there that would prevent it from starting.
At this point we're kind of at a loss and lacking a solid strategy that makes much sense.