The lever getting momentarily stuck and then freeing up could have been due to the problem Markus describes - I've had the same thing with manual mags and not-the-right-end cap. But if all appears well and the cam ring and cable are properly located and working smoothly, I'd have a look at those HT pick-ups and brushes asap. Could be a tracking problem on the pick-up, or a worn brush, or a bad connection to the HT lead itself, etc. Swapping bits round will tell you what's dud - if the problem swaps sides as well. If the problem persists on the same side, then things get more fuzzy, with fuel and valve issues starting to come into it.
Sparks are in fact weaker when the mag is other than fully advanced (the ATD was invented to avoid this by maintaining a constant relationship between armature position and points opening - but 'sporty' bikes were deemed to need lots of levers, just like people in cars wanted loads of gauges!), so an ignition fault will truly often show up with a bit of retard.