On this web page (pdf)
http://www.meziere.com/2003_catalog/30.pdf
the "Stock Car, Endurance Racer" diagram comes closest to the typical GT40, the only difference being the smaller low pressure line from the expansion tank usually tees into the large low pressure line running back to the pump because the expansion tank is located in the engine compartment. This diagram even has the correct "auxiliary plumbing" lines running from the back of the heads to the Tstat area so common with custom manifolds.
When you say the passages at the back of the heads are blocked off are you talking on the intake side of the heads or on the bell housing side? Some aftermarket intake manifolds block coolant passages at the back of the heads on the intake side. Typically this is where you install the "auxiliary plumbing" so these passages aren't blocked off. Passages on the bell housing side are EGR ports.
This is the best diagram I've seen, although it's simplistic and doesn't show line sizes, if I get time I'll draw one and post it.
line sizes
Tstat to radiator 1-1/4", 1-1/2", 1-3/4"
Radiator to water pump 1-1/2", 1-3/4"
(flow is better if feed is smaller than return)
original GT40 has 1-3/4" feed and return, many kits have 1-1/2" on both. The new GT has 1-1/4" feed, 2" return.
Auxiliary plumbing from back of manifold (heads) to behind Tstat. AN4 or AN6
Bleed line from behind Tstat to expansion tank AN3
feed from expansion tank to low pressure side before water pump (return) AN8
overflow line from expansion to overflow tank AN3
Optional remote water pump in engine compartment, 2 lines to 2 inlets of engine AN12
Here's a thread that shows "auxiliary plumbing" lines
THREAD