I would start by finding the common wire between the two coils and work your way back to the ecu. I found I had a blackened ecu pin which caused a loss of spark not that long ago.

If both sparks are lost it can only be caused by this common wire or the ecu. If either pickup was duff the bike would still run on one cylinder as it would if either feed to a coil was also lost.
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If I have to take the carbs off once more...