I'm planning on making one myself. For the PCB, I'm going to use a Madcatz Dual Force, which is basically the Kmart version of the PS1 Dual Shock. Run it through a converter and it works just fine. A friend and I have already converted a Hori Fight Stick Wii to work for PS3 doing it that way. If you decide to do something similar to that, I recommend that you use a third party wired controller. If you have some basic knowledge of how electronics work, you should be able to make it happen. If not, there's a ton of info out there on how to hack old controllers.
The only arcade stick PCB I've modded with is the Paewang Revolution, which is very easy to work with. Some light soldering and away you go. And it's dual-modded out of the box, which is a huge plus [Edit: yeah, triple modded. My PC sucks, so I don't really think about computer gaming]. The main thing that's difficult in modding one of those is working with the case, which requires some elbow grease to make everything fit. Sounds like you've got someone lined up to build a case? Personally, I'm thinking of using a cigar box or old book. I want this thing to be fuckin' renegade.
The button layout you have planned sounds pretty good, as far as I can tell. If you use an older controller like I'm doing, you won't have a home button. My current stick uses Sanwa 30mms. I like the size of those but I think 24mms would probably be just fine, especially if you wanted the jump button to be bigger. I don't know about cherry switches, but they have quick disconnects. The crimp connectors sold by Lizard Lick aren't very good. If you can find 7/64" connectors at Radio Shack, you'd be better off using those. I used 22 gauge stranded wire, but I'm not sure how much. It was a thing from Radio Shack that came with 3 spools for something like $7, and there is plenty left over. Other than that, you'll need a soldering iron and 60/40 rosin core solder, a wire cutter/stripper, a set of pliers for the crimp connectors, and maybe a solder sucker to remove excess solder. A set of helping hands is comes in extremely handy, but you can do it without them.
Looking forward to seeing the result. Bon voyage to us both.