WELCOME!
The water pump should be able to be found at any large parts jobber (if you have difficulty-get back). I would keep the old WP as it can be rebuilt and have matching numbers if you are that dedicated to origionality. It is different from the FE. The block thermostats were deleted from service in 1963 (no longer available for service)(although they were in new assemblies as late as 1965). They are not needed although the coolant divertors are.
Did you perform an ALT upgrade? What type of ALT is on there now? Can you see any stamping I.D. Nos (or amperage) on the case at the main mounting bolt?
I am going to refer you to another message board that specializes in older LINCS. Someone there should be able to help you with the vacuum tubing and weatherstripping.
http://www.thelincolnforum.net/cgi-bin/ultimatebb.cgi