Im changing the Air Intake Manifold on my 1996 4.6 Mustang?
The 4.6 does not have cap and wires like a push rod v8. It is a coil on plug design. I had to change mine at 58,000 because in '99 it was a poor design by Ford and the thermostat housing was plastic along with th rest of the manifold. It crack and i lost a lot of coolant. If that what you have, upgrade to the 2002-2004 manifold. Ford fixed the issue by making the thermostat housing metal.
Anyway, while you have it it apart, its good to go ahead and change your plugs. Check all you fuel lines and rails to make sure they are in good working order. When i changed mine, i did a complete upgrade to all the induction system. I put on larger throttle body, ported plenum, larger mas air sensor and cold air intake. it wold really help your car breathe for being an high mileage motor.