Maybe I didn't explain what I meant by "alignment" clearly here. The cam gear is parallel with the crank gear, but it sticks out a little farther so that the inner 2/3 of the rear cam gear meshes with the outer 2/3 of the crank gear. Neither gear contacts the other all the way across its width.

He said that gears don't have to be exactly in line like chains do, and he used transmission gears as an example. As you shift, various gears move in and out of position and they don't all have to fully mesh across the width of the gear in order for them to do their job.

 

I understand but I have not experienced the problem. Are you retaining the thrust washer behind the cam gear that was used with the chain drive? If so, you should toss it, not used with gears. The cam and pinion gears on some of the gear drives I have installed did not mesh 100% but most did and those that didn't were not off much.