Well you are lucky enough to have one side tieing, so adjust the missing side needle to be the same travel as the tieing side. This includes lateral adjustment. The needle head should ride in full contact with the intermediate gear facing. Run it through by hand to check this. Remove all twine and hay. Then have someone turn the flywheel VERY slowly after tripping the knotter drive while you observe. Watch the needles rise to full position, tucker fingers swing past the needles, billhooks open and close, and the wiper arm shoot across the billhook jaw. The drive chain you broke has really nothing to do with a mis-tied knot. All it does is supply work energy to the knotter gears. The knotter could care less where the plunger is (Your wallet probably does, though). Chances are the tucker fingers need to be realigned so they are dancing togther with the needle lift cycle. Then load up the twine. First time thru, the bill hooks should bring the twine from the needle and place it over the notch in the twine disk. I'll bet that's the part of all this that's not set up right.