But also remember this: The more uneccessary breaks in your audio chain... the more it's going to bleed sound out of it. Having a seperate jack on your pedalboard seems kind of uneccesary to me sine you're going to have an input for whatever pedal you choose to put first.... You could use that pedal as your input, then put all the rest of the wires under the board. It would pretty much be the same thing. Without having an unneccesary jack that will bleed sound.
Me, personally... I like my pedalboards to be versatile with a lot of things that aren't permanant like brackets and holes. I have two 4" strips of velcro across the top of my pedalboard that allow me to attatch and detatch any pedals I want... Giving me the ability to change my chain very quickly... The only thing that is peramant is the placement of my wah.
Designing stuff like this interests me quite a bit so if you're interested PM me or get ahold me on AOL or something and maybe I can make up some technical drawings that better explains what I mean... Sounds like a fun little project though and you've got some good ideas.