Let me share my experience with CB350 with you guys.
Before I rebuilt the engine I got all the possible info I could, Honda and Haynes manuals, and also several articles from Classic & Motorcycle Mechanics (Glenn have now them all if you are interested). Well, in one of the articles of CMM, they said that the official shop manual was wrong with regard to the camshaft bolts, they should be installed the other way round.
Camshaft bolts, not only are high tensile, but also are different. One is threaded all the way, the other has a "pan", a part of the bolt not threaded from the head. Since I read that I wrote down a mental note to myself: "never forget this when the time comes".
Several months later came the time, and I didn't forget about it, and even when I tried to install the bolts opposite to what the Honda manual said, there was no way. If one went in, the other was out of alignment. I was positive I should be doing something wrong, because if the skilled people at CMM found the mistake and published it, there should be a mistake. But the fact is that it was impossible to install the bolts that way. BUT, if I turned the camshaft sprocket 180º, they would go just fine. The way to know which bolt goes where was that the bolt with the "pan" had to go on the sprocket hole that was not threaded, and vice versa. Seems that the bolts are not 180º apart but a different angle -say 177º-, so if you put them wrong they will never align. That is, Honda designed them in such a way that you can not install them wrong even if you want, that whay the "TOP" mark on the sprocket will set the lobes in the right position.
I don't think there is a position for the advance mechanism. Pistons are 180º apart and so should the lobes on the advance mechanism, so it shouldn't really matter which way it goes in. If memory serves me, there is a slot in the camshaft for the mechanism to go in so there shouldn't be more than one way to install it, but it has been a few months since I did it. I put my mouth -not my money- for crossed coil wires, but considering the experience you have with CB350's, I don't think it is such an obvious mistake.