Part #7 has a reduced diameter at the end that the hole in part #5 fits onto. It can be a bit tricky, as the spring is fighting against you. You have to hold #5 in place on the end of #7, then fit the washer and tighten the nut. Also, if #7 is on backwards, the "shelf" will be facing the wrong way, so #5 won't fit over the end.
There are two dowels: the second one may be stuck in the cover? Notice that the hole on the right side is bigger; that's where the dowel fits into. The dowels are necessary to properly align the cover on the shifter shaft, and if one or both are missing the shaft may bind.
Was there a gasket when you took it apart? If the gasket is missing or too thin, the cover can pinch the shaft, again causing binding.
The notch in the outer disc on the end of the drum is the neutral detent, and the small roller drops into the notch when in neutral. I'm guessing the misalignment is what caused the problem all along, and you may have gotten very lucky.