I would have gone for the low tension lead also as a start but this looks to have been ruled out.
I have had a friend who had terrible trouble with a Ducati about an hour after he bought it and we headed doff on a rally (have mentioned this before but it may be worth a look). His bike missed and farted like you wouldn't believe, one exhaust started glowing red hot and I flagged him down. We limped to the rally site and the bike shop sent out a mechanic (good on them). He found the fault was water down the spark-plug holes, he thought it got there by the bike shop when they cleaned it with a pressure cleaner (hate those things on bikes) and water got under the caps. Dried them, it ran beautifully.
Also thinking about, it if it was fine before the ignition repair (and the bike shop lackey didn't do you the favor of water-blasting your bike) and it missed afterwards I wonder if its an earthing issue? May not be enough to kill the lights and dash noticeably but may be dropping the ECU in and out? Easy to check that with some jumper leads.