G'day mate, it does sound electrical but, as you said it was bogging, I would be cleaning the air filter first, if it is dirty to the point of reducing air flow, the engine will be running rich.
Probably best to start with your spark plug, check your plug cap and lead. If you have the service manual you will find the test values for the coil, cdi and stator so you will be able to check them with a meter. Did this happen soon after the cdi derestriction?
With shorting the rev limiter I have been told it can cause problems, though I didn't have any and other members have not had any problems that I am aware of. There is one member who was having no end of trouble with cdi's who ended up buying a custom tuned one from Sutai. When I first bought my scooter it was dificult to start after sitting for ten or twenty minutes when warm, this is what brought me to this forum. After going through various trials and errors I replaced the cdi and now starting is not a problem.