Okay maybe this will help, maybe not...
When dealing with AC current you don't have a positive wire and a negative wire per sey. AC is a little more complex as the wire is constantly ALTERNATING between positive and negative current, hence the name..
Single Phase AC Current like in your home uses a hot wire, and a neutral to power things like lights, it has one wire that constantly alternates between positive and negative.
Dual Phase AC current carries more power such as your stove in your home, this setup uses two wires, however their pulses or cycles are delayed to deliver more steady power between pulses.
Three Phase AC current is what's usually used to carry AC power to your home or power large AC Motors, the pulses in three phase are delayed by 1/3 again to allow a steady output.
Anyway the point of all this is:
It looks like from that diagram the polaris stator is a three phase stator. Thus the rectifier setup is going to be looking for a three phase input, or power coming in on all three yellow wires. As long as you're connecting the yellow wires to yellow wires the order shouldn't matter much.
That being said if you only have two yellow wires coming from your stator I don't know if just connecting them both will result in the rectifier putting out enough usable DC voltage. In short what the rectifier's job is to do is to take the Alternating Current, and via some diodes redirect the electrons so that they're all going the same way (Direct Current)..
Three phase stators produce much more usable current than other designs, this is why they're favored. Below is a simple diagram of how your rectifier works inside:
R S T represent the three individual phases coming out of a typical 3 phase stator. The diodes act as 1 way valves for current preventing the positive and negative electrons from alternating once they reach the rectifier. Once a positive pulse travels in on R S or T it can only go up (on the diagram) through the diode and out on the positive wire. When R S or T produces a negative pulse the upper diodes block it and it can only travel out the negative wire. (leaving the rectifier)
In theory it should work with only two wires although it ultimately depends on how much juice your stator is putting out as to how much DC current you'll get.
I hope this helped, and didn't further complicate what you're trying to do!
As an alternative, you could always put the largest battery you could fit in there and just charge it between rides. I had an old 87 banshee that I put a battery on for LED headlights and a GPS, it lasted a long time between charges, when out on a ride I would use jumper cables to the truck to charge it when no battery charger was an option.