I replaced the internal resistors on all 4 plug caps after having a problem with one while on a fast ride years ago. I used same length brazing rod & it made an immediate difference.
It was only a few years later that I had what I thought was a similar problem & replaced all sort of parts in the carbs, ignition leads, spark plugs etc.
In the end it was the standard plug caps which, when cold gave no problem. Once hot though, the ceramic caps on at least 2 caps opened up along the seams & the spark energy from the high output coils crackled to the cylinder head, which was quite a sight when viewed in the dark with the tank off. Once i'd replaced the caps using ones from a GSXR750 everything worked ok.
Not sure if long straight NGK plug caps, either the black ceramic or the waterproof silicone ones are best for the Exup engine. I've got a silicone rubber one on my XR-SM & it keeps the water out & isn't affected by lots of water.
Note: With the NGK silicone plug cap, it also comes comes with a resistive element which I replaced with a length of brazing rod with no issues with ignition.
http://www.ebay.co.uk/itm/NGK-SD05FM-R- ... SwYmZXEK2A