i doubt that small change in manifold geometry would cause your overheating. A lean condition COULD cause some heating.. thus a gasket issue might have contributed.. if the rad is plugged.. that would deffinately be an issue. the rad shop hopefully will rod it od and test it for you.
oce you get it back, check your carb and manifold gaskets and see what ya got.
if you have a non contact temp gun.. check a few spots and see what ya got.
also.. do you have the oem heat shields in place around the manifold?
you can also see if your pump circulates water with a hose-off test. though i rarely see an impellor rust completely away.. I have seen one that nearly did..