Slight misfire - plugs?

[Gnasher]

I will 'drain' water from carbs later on

Is there water in the float bowls have you looked?  If so this would indicate that you have a problem with the tank and that will lead to blocked pilot jets!

but just checked the plugs and they are CR9E instead of CR8E, could that potentially cause the problem

No you can fit either the 9's are slightly cooler than 8's you wont tell the difference is normal everyday use in the real world.

but considering what was done to the cooling system I wouldn't take their newness for granted

What has been done to the cooling system?

it normally happens only when it warms up, same with the misfire, less of a manifestation on cold engine.

This is typical blocked pilot jet symptoms as has been said.  A simple way to find out which ones ride the bike for a mile, stop, get some water in a spray and squirt the downtubes one at a time those that dont hiss are missing.

I should have start with this part, shouldn't I?

Yes

As for the coil pack being faulty this is the last thing to check, I've been working on these bike since they were introduced the coils are very very reliable. The polarity is marked on the case.  A very quick and easy test is to swap the packs over if the problem then jumps it's the coil, that said it's possible the lead is the issue as these do degrade over time mainly at the point where they enter the plug cap.  Again very simple unscrew the cap trim off about 10mm and refit the cap. 


I dont believe your issue is electrical it's already been said check the pilot jets!