Use your stock carbs. I ran VM34's on my XS cafe. They were great, but if you have good stock carbs, start with those and get the bike running.
Then decide if you want to jump to the VM's.
MikesXS cartridge emulators are a nice add for the front suspension, but some work drilling out damper rods etc.
I think regardless of how you lower the front, the handling will be the same (unless you also lower the back). Whether you use Hugh's lowering kit or slide the forks up the tree, the geometry is the same. So fine tune things before you bother with lowering kits. Then you can decide the right setup.
I'm working on a rigid XS bobber myself, and have Hugh's 3" lowering kit, but I haven't installed it yet. I'm waiting to get the bike built, engine in, on the ground to see just where the suspension settles before deciding to do anything.