The GT40 intake is actually a really good intake. The only reason I didn't buy one is because they are a little expensive. But if you don't mind the cost, you may want to consider buying another. Plus the tubular runners just look cool.
Other than that, I'd say probably the Edelbrock Performer RPM II (since you do have a 331, otherwise I'd say just the regular Performer).
As for the lifters, go to Summit Racing - High Performance Car and Truck Parts | 800-230-3030
and look for the FRPP lifters. They are cheap and probably the best lifters you can buy. They also have the pushrods, but they probably aren't really necessary to change. If it was me, I'd probably go ahead and do it anyway though.
For the water pump, I'd probably just get a stock replacement.
EDIT: Here's some links to the parts.
Edelbrock Performer RPM II