The condensor is, indeed, there in part to protect the points.
When the points are closed, current is flowing thru them (and thru the coil first) to ground. When they open, that current flow stops, but while they are just barely open (think microscopically), there is certainly enough potential to jump that tiny gap, ie a spark. Think of it as drawing a tiny little arc like an arc welder. Now, that spark is still current flow, and the whole point of opening the points is to STOP current flow so that the resulting collapsing magnetic field in the coil's primary winding will induce a current in the secondary windings enough to jump the spark plug gap - spark the plug.
In addition, that little spark at the points will eventually burn their surfaces up.
The condenser serves to 'absorb' that momentary voltage surge at the points until the air gap is sufficient to block a spark.
As for troubleshooting a weak spark on one cylinder, I'd be certainly swapping parts side-to-side as mentioned. Spark plug, ignition coils, condensers, etc. And only one component at a time, of course. That way, you'll KNOW which component may or may not be bad.
And, timing difficulties won't cause a weak spark. They'll only cause the weak spark to happen at the wrong moment. A different problem, which of course needs to be fixed, but not the cause of a weak spark.
Good luck, and keep us posted.