Update!
So far I've been liking it best with 3 magnets pulled on each side of the pickup. It avoids most of the phase cancellation and sounds much more like a single coil. Having all the magnets makes for a really cool and unique sound, however.
The 2nd prototype is on its way! This one will have a 3+3 cover so it doesn't look strange. I'm going to check some specs to find out how pulling the magnets changed that as well. I think I'm going to leave the wind really similar if not as identical as I can get it. The bridge side coil is 0.2K hotter because it is slightly closer to the bridge, but I may reduce that difference a bit.