Hokay. A fuse is meant to protect the wiring, switches and the load (motor, etc) in the event of a short. That means it should be as close as possible to the power source. So for each circuit you go batt> main kill switch> short wire> fuse> long wire> control switch> load> ground.
You can simplify that by using terminal strips, like this:
Avoid the cheapie white terminal strips with the little set screws in them, those just pinch the wire and can often create high resistance.
On a real simple race car, I'd keep the number of switches to a bare minimum: ignition, lights, wipers. I have found with rotaries that being able to turn the fuel pump off is A Good Thing. So I'd have a toggle for that but run the ignition directly off the kill switch (also see below).
Relays are for high draw items like lights, heater blower motors etc. On a gutted 1st gen RX7, there's not a whole lot which will need relays. Even the fuel pump only draws about 3-5 amps, meaning a toggle switch will work fine. The ignition coils draw a lot of power, but instead of a separate toggle switch or relays I'd suggest wiring them directly to the big output terminal on your kill switch. If you want to fuse them, then I'd look into those big maxi fuses. I'd go 40 amps and put them where you can get to them easily, plus carry some spares. You might even consider circuit breakers for that particular use, again mount them where you can get to them easily.
I'm going to start a E36 M3storm but welding cable, while nice, is not really necessary for battery cables. Those premade battery cables from the parts house will work just ducky.
On alternators: for an RX7 to make it work all you need is a wire directly from the alternator + terminal to the battery +, then there are two small wires going to the alternator. One of those needs to have power when the ignition is switched on. Unfortunately, i do not remember the color so you probably need to grab a wiring diagram to find out for sure which one it is. The second small wire is, on 1st gens, a power output. This goes to a relay which does all kinds of crazy stuff and also runs the charge indicator light. The problem: just about every car out there uses that wire as a ground instead of a power wire. There is a way to make it work which involves a relay and some other funky stuff. I can post a diagram if you want to wire in a light, or you can leave that wire disconnected (insulate the tip of it!) and use an ammeter in the dash.