Is the hole in the intake a hole and I need to replace it, or is it missing something that goes there?

Is it a plastic intake, is there coolant coming from that hole, and does the engine run?

Yes the engine still runs, and it is a plastic intake

In fact, there is a service bulletin and sebsequent recall that may apply. The recall was only good for 7 years from the vehicles warranty start date, which yours would be out of.

The bulletin info follows:
Intake Manifold - Cross-Over Channel Coolant Seepage


Article No.
02-2-2

02/04/02

^ COOLANT - COOLANT SEEPAGE AT INTAKE MANIFOLD CROSS-OVER - VEHICLES EQUIPPED
WITH 4.6L 2V ENGINE ONLY

^ ENGINE - 4.6L 2V - COOLANT SEEPAGE AT INTAKE MANIFOLD CROSS-OVER

FORD:
1996-1997 THUNDERBIRD
1996-2001 CROWN VICTORIA, MUSTANG
2002 EXPLORER

LINCOLN:
1996-2001 TOWN CAR

MERCURY:
1996-1997 COUGAR
1996-2001 GRAND MARQUIS

ISSUE
Some vehicles may exhibit an Intake Manifold crossover (first runner) coolant seepage condition. This may be caused by a crack in the Intake Manifold coolant crossover.







ACTION
Inspect the suspect Intake Manifold for a coolant leak at the first runner cross-over area (Figure 1). If coolant seepage is found in this area, order the appropriate Service Kit and install parts, by referring to the appropriate Model Year Workshop Manual (Section 303-01).

4.6L 2V INTAKE MANIFOLD

INSPECTION/REPLACEMENT

Refer to Figure 1 for inspection of coolant seepage.












If seepage is found, order one of the following Service Kits to repair.

OTHER APPLICABLE ARTICLES: NONE
WARRANTY STATUS: INFORMATION ONLY
OASIS CODES: 402000, 499000

The hole is in the very back of the intake by the cylinders

If there is coolant coming from the hole, then I would say that the intake needs replaced. If you are unsure, then a pressure test of the cooling system is recommended, to confirm.