Ron,
You're definitely on the right track. The supplied diagram is an excellent guide, and you should simply follow it. Although the GT40 differs in detail and is much more complex than a Mustang, at the end of the day, a Ford is a Ford. There's a Gozinta and a Gozouta, and you just need to make sure you hook up the right hoses to their appropriate fittings.
In answer to some of your specific questions....
Weber intake manifolds follow the same design philosophy as standard carburetor intakes, with some detail differences. Aftermarket intakes have a single water outlet to the radiator, equipped with a conventional thermostat, while the original GT40 intake used a pair of smaller outlets. A special Y-shaped pipe joined the two small outlets into a single, larger pipe, and a thermostat would then have to be fitted inside of another fixture downstream of that (the originals didn't appear to have any sort of thermostat, if the parts book diagram is accurate).
Water outlet to the heater, on the original cars, came from a fitting attached to the aforementioned Y-shaped pipe at the front of the motor; water inlet from the heater to the water pump was achieved by a fitting on the pipe which connected to the water pump inlet. Both were in the engine bay. (The SPF setup follows the same design philosophy, but relocates the inlet to the water pump--instead of being right next to the pump, it's located in the pipe leading to the radiator, so the fluid is sucked from the heater, then through the radiator, then back to the water pump).
Assuming your Weber intake is one of the aftermarket types that use a standard single water outlet with a thermostat, you should plumb your car the way the Mustang is set up (and the way the SPF diagram above indicates). Water outlet to the heater is achieved via the port on the top of the intake near the thermostat housing; a dedicated fitting goes here, available cheaply from all Mustang parts sources. Here's one:
You can get it here:
Mustang Parts from Mustangs Plus :: Heater & Defroster :: Heater Elbow :: 1966-70 Mustang 289/302 Heater Elbow
Although every Mustang parts shop in the world carries them.
That goes forward to supply the heater core. The outlet from the heater core (according to the SPF diagram) goes into the pipe which feeds the radiator. Then the 5/8 inch hose on the bottom of the expansion tank leads back to one of the two smaller inlets on the water pump (the other is capped off).
In short, follow the diagram above and you can't go wrong. If you want to be super-duper authentic, you could follow the original GT40 plumbing scheme, which can be seen here:
Note the electrical switch, part #32 in the diagram above. I *think* that is the temp sender for the water temp gauge, although the parts book describes it as a 'temp control'. I don't see how that switch would control anything, unless...wait a minute, no, that's probably the switch to turn the radiator fan on and off thermostatically. Does anybody know for sure?
You'd want your water temp gauge to be reading from the engine, not the radiator outlet anyway. You don't care how hot your radiator is, all you care about is how hot your engine is....
Oh, and by the way, if you're going to install a manual heater shutoff valve, make SURE that you install it in the supply line TO the heater. I had one installed in my GT350, and made the mistake of putting it on the outlet side of the heater. It worked just as well, from the standpoint of preventing any flow through the heater. But one day I was running the car on a chassis dyno with the valve closed, and saw water dripping onto the carpet--at high RPM, the pressure was extreme, and the heater core was practically bulging under the strain. Not good! I replumbed it that very day.
More than one Pantera has been wrecked because of a burst heater hose in the cabin--it always happens when the RPM is high and the testosterone is too. When a heater hose (or core) lets go inside a small cockpit like a Pantera or GT40, the result is that superheated water sprays all over the occupant's legs, burning them severely, and the windows all instantly go completely opaque, so you can't see where you're going. A split-second later--BAM! And you're into a wall or tree or another car.
So heater hose shutoff valves are a very good idea; when Panteras run on track events, we require two of them, on the inlet AND the outlet side. Mechanically there is no reason why a single valve on the inlet side (to the heater) wouldn't suffice, but it's difficult for tech inspectors to tell at a glance that the valve has been installed in the correct line; putting them in both lines is a belt-and-suspenders solution that makes the tech inspector's life easier at the same time.
And remember that hoses don't last forever; plan on changing your heater hoses, at least, every 10 years or so....
