Just a fair warning, I'm probably going to throw a lot of links into this post.
The easiest way I would see this working is to get something like a pre-made motherboard tray so most of the stuff that requires decent tolerances are already done and figured out. Mountain Mods has trays already figured out, among other cool motherboard things. Or maybe even a Lian Li tray.
Another idea might be to get a pre-made front panel and I/O setup if you don't want to go about sourcing power switches, reset switches, USB connectors, the wiring, and stuff like that. I know Corsair sells both for a wide variety of their cases.
Oh, and a pre-made hard drive cage would make life significantly easier since everything is already the correct shape and size already. Once again, Corsair makes that. Same for 5.25" bays if you want them (I wouldn't personally).
Passed that, it pretty much depends on what you want to do. I'll throw out some parts/ideas that might interest you as I think of them.
Modmesh is pretty amazing for making vents and grilles quickly. Cut it to shape and weld/screw/rivet it in place and you're done pretty much. Drill holes for fan screws as needed. There's a whole slew of different types available, so you should be able to find anything you are looking for.
You'll probably want fan templates so you know you're making the right sized holes with the correct spacing.
Power supply template as well.
If you want things to be permanent you'll want a rivet gun and rivets. They're actually pretty easy to use, drill a hole, put in the rivet, squeeze the trigger a few times, and you're done. Amazon probably has some for cheap.
For raw material for panels you can actually get that stuff on Amazon. Price-wise plain steel would be cheapest, followed by aluminum, then stainless steel. You could go crazy and make one out of magnesium, but good luck if something ever catches fire in a magnesium case. Most cases I've seen appear to be made of 1mm or less SECC (stands for Steel, Electrogalvanized, Cold-rolled, Coil), but I would assume that any steel sheet that's 1mm or thicker would be strong enough. Amazon has some plain steel sheet that is pretty thick for pretty cheap.
For connecting the "frame", I think regular angle steel/aluminum would be easiest. to attach the bottom, back, top, and front pieces together. I've seen a custom case that did that then used some more angle up the sides with triangular pieces of metal attached to the corners. The triangular pieces didn't do much for structure, but it did allow for the bottoms of the side panels to slide behind so they wouldn't fall off the bottom of the case. The tops of the side panels simply had small magnets attached to them. I'll try and make a quick sketch in Paint or something to illustrate the idea better in a little bit.
It's pretty straight forward once you get a plan figured out. Without things like a drill press I would strongly suggest going for the pre-made stuff for things that need good tolerances, like the motherboard tray and cages, the tray at the very least. Now off to Paint!
