As both inner plugs fire from different coils I'd be loathe to blame them.
This "hot start issue" which Kit dug into pretty deeply seems a 650 thing, I still don't think Kit knows how she cured it she just did.
![Cheesy :D](http://forums.sohc4.net/Smileys/default/cheesy.gif)
If you haven't had the carbs synchronised yet that would be my next move, they sound like they are pulling against each other at speed, this also gives a pretty crappy idle but if you've never seen or heard a 650 on-song then you wont know if your is good or not.
That starnge exhaust note could also be carb sync related, if they don't pull as a team you wont see the best out of your bike, the difference once done is amazing...like someone just gave you a new bike.
![Grin ;D](http://forums.sohc4.net/Smileys/default/grin.gif)
Another thought occurs, if the carbs are out of whack with each other there will be residual gas unburnt at stop, this will give a pretty rough start up again as the mixtures will be off.
My Clymer bible doesn't give any test for the pulse generators sorry, I guess if you have spark then you have PG's working.
Did you look at my suggestion of realigning the PG plate or rotating it slightly either way to improve your bikes' issues?