TCI failure and impact on engine performance

I ride a XV535 that has been acting up the last couple of months. Symptoms include the perenial Yamaha popping while traveling at a steady speed, engine missing on exceleration (1st through 4th gear), and missing at a steady speed ie around 45kph in 3rd and around 70 kmp in 4th. The popping could be unburnt gas igniting, however it is not loud like a backfire.

The poor performance is not constant. You can climb on the bike and it works great...no problems. At other times it runs great but after it is turned off overnight or just turned off to fill it with gas it will start to run poorly. I've had it into the Yamaha five times trying to resolve the problems. They have focused on the carbs, put in new jets, gaskets etc but to no avail. The mechanic has just about given up in frustration. We are now thinking that the problems could be caused bu the Transistor Control Ignition System (TCI). I have been reading the Clymer Service Manual and it states that while these types of performance issues can be caused by worn or improperly adjusted carburators, the "odds are far better that the source of the problem will be found in the ignition system rather than the fuel system".

Has anyone out there had a TCI failure, and if yes, what types of performance problems did the engine exhibit?

Thanks for the input.

RM