Hey Duceditor, I have pretty much the same setup as you on my SC with your exhaust mod using just 2 holes. The fatduc is amazing for an $80 part, will try slightly leaner after I put a few more miles on.I find the bike runs best with the Fatduck at the as-delivered setting. Technically I expect it is a little rich - evidenced by the smell of unburned fuel. But for the style of riding I currently prefer it is perfect.
That said I presently have mine set a little leaner, and that to boost the mileage. Without the Fatduck I was averaging about 52 MPG. With the standard, as delivered, setting on the Fatduck it dropped to the mid to high 30s. With my present compromise setting I am seeing mid to high 40s. The price of this is a loss to taht oh so right creamy smoothness at low RPM.
Truth is that mid to high 30s is pretty normal fuel mileage for a 1 liter displacement bike. But with gas stations few and far in between on NH's back roads getting another 8 to 10 MPG is helpful, and the $s saved is a nice added benefit.
As to tuning your own Fatduck, just play around until you get the compromise that works well for you. You won't hurt anything. When the bike feels "right" you've got the best set up and if MPG is important you can simply mark that place on the dial and go leaner when you need the extra mileage per tank.