No reason it shouldn't, Mike. With the ignition out of the picture, all that matters is that the genny, regulator, battery and light bulbs (DON'T forget the light bulbs!) are 12v.
Two thoughts . . .
Pay attention to whether your regulator is polarity sensitive. If not, no problem. If so and there is a choice, at 12v I'd opt for the negative ground if it were mine.
You might not need much in the way of a custom harness. Look at BobM's #4 diagram, but I think you could go with the harness for the magneto setup and simply swap the wire that would normally run from the Field terminal up front on the cutout relay back to the 4-position switch, and use that wire from the Load terminal on your regulator back to the fuse in your setup. Then all they'd have to make up as "custom" would be the Field jumper between the genny and the regulator.
A reputable company would charge you that way -- their standard magneto harness plus one wire. Don't know where you're shopping for the harness, but some would tack on a pretty severe custom charge.
I've had two good experiences with Agri-services (wiringharnesses.com) and from what I hear Brillmans's is on a par with them in terms of quality of goods and bein' good folks to deal with, too.
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