[FWB]

look at the center contact of your msd cap carefully, is the button still there?

if so, then check your voltage to the msd box, they are voltage hogs and if they are not getting enough power they do strange things, i would see what kind of output your alternator is giving you and is the battery up to snuff, where are you getting power from going to the msd.
by connecting the timing light to the bad cly, you introduced a temporary field giving the idle up condition.
the problem seems to be ignition, or power to the ignition.....