Wow. Good observation. I am glad you can get it sparking with both plugs in.
Standard operating procedure is so second nature, I never thought about it being the problem.
Yes the clutch should be cleared before kicking it. Then bring the engine to TDC, or just a tad past. Then you bring the kick starter to where the lever is about parallel with earth, by using the free clutch. Then re-engage clutch, and swing through "the kick start". The inertia of the flywheel should than do the job.
One thing. The kicker may not be engaged just right, inside case, for best use. But do not worry too much about that for now, since you can get it to spark.
Another thing. Since the bike has been sitting, the primary may have been overfilled, so that now there is a lot of oil in the sump, and now that excess oil is slowing the rotation of the crank.
I hate to say, try draining the sump since there is always the chance of introducing a particle of dirt, but perhaps in this case it is warranted. Just be very careful to get everything clear and not touch the plug to anything on the way in. If you do drain the sump, measure how much came out, just so we can know, if that was an issue.
It is has been suggested that with starting procedure you go just a tad past TDC. This allows the momentum to build so the swing (actually your foot will move slightly forward at the end of travel). Embarrassingly to me, John has told me that he has taught 5' 1" 110 lbs girls to start their bikes in this fashion, without taking a a hop. This he mentioned to me as I was starting my bike.
I still do the hop when bike is cold. I have tried the swing so many times, and I can not get it.
I still think it would be a good idea to have the battery load tested, just as a matter of course, at the start of each season, when one has an EI installed.