(Warning: this is kinda long, but I figured out something kinda interesting)
In regards to the Bill v Jer or Bill v Matt Final showdown, I think Matt and Bill would make more sense.
Yes, Jer could have killed Bill, but the way I see it, at the end of Return of the Bill, Jer was grabbing the dagger to protect himself from Bill, as Bill held onto the katana to protect himself from Jer. It was mutually assured destruction. Also, Jer has the powers of the shaolin warriors, but he doesn't have the discretion to determine when and where to use it (SEE Pull Yourself Together), so he's not really considered to be as big a threat, because Bill has Jer stunted in his ninja-skill education.
How does this disprove the "Jer was a ninja in two videos, so he has to be" theory? Well in "Lock Out", Jer is only using his ninja disguise to be a bother with the room key. And seeing as Graham was able to take it from him, he's not a good enough ninja to circumvent a defense. As for "E-Zed Industries", that was in Jer's early days of training, and if you notice, Paul is the only one who looks like he is visibly killed, while Morgan and James look merely subdued and by the "ninja". Paul, however, is dead already, and it's easy to return him to that state. As for Graham's character, Matt is the one who summons the ninja, and ninjas only answer to their own kind.
Also Matt moonlights as a student at the same academy as Naruto (I'd use the name, but I don't watch crappy overhyped anime, or anime period), has the ability to show up in different states and places withing a fraction of a second, and has on one occasion in particular, killed many people in order to survive. Sure he looked like a WoW battleaxe wielding PC, but that was all a clever ruse to allow him to kill and kill again.
So in the end, it isn't Jer, but MATT who is the real professional ninja, and therefore Bill will have to battle Matt in a post-apocalyptic street battle to prevent the destruction of mankind.