Sounded like an electrical problem, but you say the spark is painful, sorry I mean good I can't see why it would be a fuelling problem at the exact time of a gear change, doesn't make sense. With a late gearchange, and higher revs maybe it's a cam chain snapped. Try and get a compression test done to check. Sorry, I don't know your bike, so I can't be more specific. Hope you sort it soon.
I say fuel problem only because as I cheeked to see if fuel was present and I opened the overflow valve in the carb and it was orange..I must have the only bike in the world to not have a fuel filter, I'll take the tank back off tomorrow and see if I can see the valves moving.
take the plug out and pour a little petrol into the cylinder head, plug back in, lead on and try again. if it fires up for a few seconds then dies as you then say it could be a blockage. And by a little petrol I mean 5-10 ml. good luck.
Spray carb cleaner into the air box then try to start it, Best to try spraying it in while the bike is turning over. Pouring fuel in will just flood it. Check neutral switch, and side stand/clutch switch.
