I'd agree with all of that but, since it is very late, I shall wait until I've slept to write a long(er) answer. For now I'll just go with this;
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For example, the stance Ichimonji, and the punch we so often make from that stance is in no way combat effective, and we know this to be true.
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The punch from Ichimonji we use has one use, discipline.
The 'lunge-punch' as it is commonly known by outsiders and insiders alike has much more than one use and indeed has a very good reason for being there. Much like Ichimonji itself.
Not only is it the quickest punch from A to B but the vertical punch is also a feature of Jeet Kune Do and Wing Chun, one style and a concept known for combat effectiveness.
It is not the punch itself, only the way we deliver it in training.
No one would ever stand in Ichimonji (at least not in the classical way) and throw a hefty lunge punch... of course not! However over time the stance retracts and the punches can be used from a retracted kamae from varying angles, at varying speeds and without looking at all like the 'training punch' which, I agree, is used only for, well, training.
Thus I would, speaking from personal usage, disagree with this;
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instead things such as this are simply for use in training.
And lastly;
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To continue, the contrast would be that every technique should be resisted as best as possible. Imagine how little we would know of ninjutsu if every time we tried to do a technique, the Uke would stop it.
A) If you're doing it correctly then they shouldn't be able to stop it because each piece should have slipped into place.
B) Full resistance should be the overall goal. Gradual resistance should always be applied to see exactly how well you and your technique would work against a resisting opponent.
That's all I've got, for now. I'll pick apart more of your post later.