I confuse my self quite often
The long pipe which has rusted for you is the heater feed, the return goes parallel to that and feeds the back of the water pump, well it did on my 3.5 flapper engine.
If you don't have a heater you can block off the port that this pipe screws into as long as you have the bypass circuit connected.
You could use the bypass outlet to feed the heater, but if that would then be replace your bypass circuit then there shouldn't be a heater valve to cut off that flow. I guess you could use the bypass outlet to feed both the heater and the bypass circuit but with the higher resistance of the heater matrix I don't know how much hot air you'd get in the cabin.
I think the main difference with the older manifold is the injector holes, the newer manifolds designed to take an o-ringed injector. Also there is a flat for the idle control valve to bolt to which is not on the newer manifolds. If you can get the injectors to fit, and have some sort of idle control then I don't see any reason you can't use the newer manifold. You'd need to check regarding to holes/threads for the sensors.
Tom.