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Well, since the knife arm was good when you took it apart, then it should not need any bending or forming to put it back together. Replacing the twine knife should have needed nothing more than some rivets drilled or chopped and some new bolts and a knife blade put back on. There are, however, some shims or spacers on the wiper arm assembly (which holds the twine knife) which may be missing or in the wrong place. That's the only reason the wiper arm ball would miss the knotter drive intermediate gear. That's the wheel with a few gear teeth on it that drives the billhooks, etc. Other than that, we're gonna need a few pictures if possible. One good thing going for you is having one perfectly good knotter. Your goal should be to make the position and actions of the "bad" one duplicate those of the "good" one.
You might want to read the manual again more closely. The manual should be telling you to bend the "wiper arm" if and only if the wiper does not contact the billhook foot. The knot is actually scraped off the billhook. The wiper arm does not cut the twine. the twine knife does. Terminology is a big factor, here. Billhook, wiper arm, twine knife and intermediate gear parts all have distinct functions and timing.