I have found one upper coil that has a weak spark but passed muster in the spark plug check thingy. I removed 1 stick coil and put an old spark plug in it The bike won't run if you take a plug out

Fired up the engine whilst holding the plug against a suitable bolt for an earth (Valve cover bolt). It had a nice blue spark. However, if I moved it away from the earth the spark would stop arcing after about 6mm. The other coils would be sparking away at up to 25mm away from the earth point. I have changed it for another coil I had lying around that gave a big fat spark.
Unfortunately, the lumpiness is still there. I have changed the TPS (and done the rest procedure), the FPC, checked each of the 4 coils is jumping a gap of at least 19mm, put new plugs in, stripped down and checked the kill switch and starter button (and put contact treatment in it), checked the ignition barrel connectors, given the side stand switch a good waggle, soaked the gear position sensor in WD40, checked all the electrical connectors for corrosion, checked for trapped fuel lines and breathers, checked the throttle body balance. Each change, check was followed by a ride out to check if it had improved. Not sure there is much left to check.
This all seems to have come to notice since the bike was Serviced and had a new fuel pump fitted under the recall. I think it is coincidental though. The only thing that I can think of is the alternator needs changing as the bearings are tight. This is due to be done next week so I can only wait and see.