Wow. I read this earlier this morning, and didn't post because I thought that maybe someone else would pipe up, and to be honest there really isn't much more I can think of that would help.
But, the first thing I would say to check is system grounds - you didn't mention whether or not the coil/CDI unit have good grounds to the frame. I'm sure you've already verified them, but it's little stuff like this we sometimes miss when dealing with projects from hell (from the sounds of it, thats what this sounds like
) It's not possible the spark is arcing somewhere else before the plug without you hearing/seeing it, is there? Possible fault in the plug wire by chance?
As you've stated, you've replaced virtually every component of the ignition system. The only other thing left to check is the rotor. I don't really know how it could fail other than loosing it's magnetic force, which is highly unlikely, if not impossible.......don't really know how you'd verify the amount of magnetic force it currently has either.
Beyond that, the only
other thing I can honestly think of that would hinder the bike from having any spark would be some type of internal engine rotational resistance that is not allowing the rotor to move past the stator fast enough. Unlikely since you just rebuilt it, but again, it's something to think about....I've had this happen to me before, but it was because the mains were virtually seized. The bike would start if I pull started it at a very high speed, but I couldn't kick the thing over no matter how hard I tried.
The fact that it pops at the bottom of your kick is odd as well....while that would point to a timing issue, the ignition should have spark irregardless of its timing....
Again, the above is just stuff that comes to mind......either way, I'd be interested to know what the fix is when you figure it out