I have an 02 4.4 and here are prices that I paid from a dealer (under warranty) for some of the items you mentioned;

Valve cover gaskets - $660
valley pan gasket and water pump - $1800

I agree with teh others, find out what they mean by tune-up. I would imagine they are referring to inspectio I or II, which costs me about $300 and includes oil and filter, air filter, micro (cabin) filter, and fuel system cleaner.

EDIT; I see that the tune-up included plugs. With that added into it, the price quote does not seem unreasonable to me. As long as they perform everything else required for Inspection II.