Hi Josh, I am also a newbie. The way I understand it, If you want the most cost-effective, best "bang-for-your-buck" 3-phase, you follow the 3-coil/4-magnet rule. (it sounds like you have) The way I understand it (and theres no guarantee this is 100% accurate) The alternating faces of the magnets should be evenly spaced out NSNSNSNS (sounds like you did that).
Each "N" magnet face is paired with the "S" face to its left, and also to the "S" face to its right. In a 6-coil PMA there will be two coils that have an N and S magnet faces directly over the two legs of two of the 6 coils. One magnet is pulling, the other is pushing. (in an oval coil, the two long sides are the legs, and the two short connecting sides are just a "neccesary evil").
You may want to check the shape of your coils to ensure the centers of the two opposing magnets are centered over the two legs of one of the coils. At the precise moment when that orientation occurs, a pulse is created.
At that moment, two other coils will have a magnet pair just leaving their two legs, and two of the coils will have a magnet pair just about to arrive.
The flux of a single magnet should normally be about equal on both the N and S sides. If you put a steel backing plate on one side, it will "pull in" the flux on that side, and strengthen the flux on the side that the stator is on. A smaller "air-gap" will put the coils closer to the strongest part of the magnets flux, increasing output, but it will also cause it to take more force to initially get it spinning.
If you add a second rotor on the other side of the stator with the magnet faces opposite of the first rotor, the two steel-backed rotors will have a very strong magnetic flux in the middle, where the stator is.
You may have free or cheap round magnets, but round magnets over oval coils means only about half the copper is getting a "flux push/pull" and the other half is adding resistance without adding any voltage. Wedge shaped magnets and coils are slightly more efficient because 2/3rds of the coil is sitting in a magnetic field, while only about 1/3rd is unused.
At least I think so...Since you have actually built one PMA, you have done more than me!