The 96-98 cars (GT's) had issues with a crossover pipe on the plastic intake cracking. The early TSB's replaced the manifolds with a newer design but still all plastic. The later designs had an aluminium crossover pipe. My car's original manifold crossover cracked at about 25,000 miles, Ford replaced it under warranty. The second manifold also cracked at 46,000 miles and it was replaced with the aluminium/plastic manifold.
After the first replacement, Ford gave me a letter documenting the first repair and extending the warranty on the manifold for an additional 36,000 miles. The second manifold was also covered under warranty, but I had to remind the dealer that I had an extended warranty.
The first incident was pretty catastrophic, I was accelerating onto the freeway and the crossover cracked, spewing coolent all over the engine and windshield. The second incident was similar to what you are experiencing, intermittant overheating.
Check the underside of the crossover pipe on your manifold. It's the first black plastic tube connecting the heads on the front of the 4.6 motor. Feel around underneath it and in the vee between the heads for any coolent.
You should be able to get a replacement manifold with the aluminium crossover at a junk yard or at the dealer. Remember to get the one for the original 96-98 heads, not the PI heads.
Larry
97-0183