Had a similar issue on a Honda that appeared straight after fuelling up in France. Turned out to be high resistance plug cap Thanks I'll have a look
Knowing Yamaha I wouldn't be surprised if it's a coil then but first off I'd clean the low tension connectors and SA tape the leads and blow out the plug tunnels. If your drain holes are blocked you'll have water sitting around your plugs causing trouble.
spray brake cleaner on your downpies mate, suss out which one aint running right first. then swap coil leads to further isolate the problem ( four and one the same, ditto 2 and three) sorry if thats saying what you already know mate, and hope you get it sorted