I've gone both routes, PT and homemade. If you are going with the Voodoo power suppy, my suggestion would be to pick up a Pedatrain Jr. It's light, angled perfectly for two rows of pedals, fits the Voodoo perfectly, and because of the ability to run cables in and out and under, a great base for mixing and matching pedals and pedal order...something you'll find yourself doing a bunch while you experiment and find your pedal preferences. And the PTs come with their own case.
Once you get further down the road and have a somewhat narrower idea for what all you want, you could look at building yourself something custom. To me it wouldn't make sense to customize a board build before you knew what your ultimate needs were.
Eat all your veggies. And don't bang the dillies.