Did they upgrade the coil to go with the electronic ignition. I did the same thing in mine and from what I understand the stock coil can not handle the hotter spark from the electronic ignition. Also the spark plug gap will change with the new ignition.

Not sure if either of these things will fix the issue but I know when I did my new ignition these factors came into play and resulted in a much better running boat. Timing was all a huge factor to get dialed in if they where not careful installing the ignition and getting it dialed in it could be off.