I have two XE specific issues with a homemade inlet manifold, firstly, what do I attach the top altenator mount too (suggestions welcome) and secondly why is there a water pipe in the way?

When considering this picture: http://www.sbdev.co.uk/Info_sheets/Cooling_systems/Cooling_system.htm

you can see there is a movement of water through the inlet manifold. Can I just block this off?
Rescued attachment plumbing.JPG