Lowering a Custom isn't a good idea. It's gonna handle like crap, and won't corner well. They already have very limited clearance (I scrape floorboards daily at stock height), and lowering it more is a bad idea. You're gonna be that guy taking an offramp at 15mph slower than you need to be because you can't lean your bike.
Personally speaking, I strongly disagree with this.......
I have monotubes up front set at full drop, which measures out to be just shy of -2.5" and current running air ride out back with a ride hight of -1" (ability to go -3.5" when parked)
With that said, I ride my bike, well, like a bike and pretty damn hard. Up here we ride the hill/mountains to coastal highway 1 to the switchbacks through the vineyards. I wouldn't do anything to my bike that would decrease its handling capablities.......bike looks good and rides/handles even better than stock. Which isn't to hard to do at all. The factory ride on these leaves a lot to be desired!
If you wanted to go lower with your bike, to improve handling and get flat footed. I'd do the following, if I were in your situation:
Front: monotubes, the lowing version will allow you to choose -1" or -2"
Rear: quality shock of your choice in 11.5"
Seat: if needed, have a the nose of the seat narrowed up (even with the frame)
Im 6'1", so I didnt lower my bike so much to be flat footed, i just wanted to lower my center of gravity and love the slammed look
Not that I know a whole lot, but from my personal experiences that would be my $.02
Suspension wise, I believe TraceyB has very similar setup. Also without problems, except maybe people flocking to her bike in parking lots to stare