I had my intake ('97 4.6) replaced 2-3 years ago, too. When I checked the Ford website, it said there were no recalls for my car. Do you have any info regarding the recall?
Also, my check engine light has been on for over a year. My mechanic said it was a 'random misfire' (he read the codes). He changed the plugs (I had done them myself not too long before, with Bosch, he said don't use them in Fords, they won't work right, use Autolite), and it didn't fix the problem. This was just prior to a smog check, and I probably just made the required run time for it to be done, as it passed like a champ. The light came back on when I was driving home!
Anyway, what all is likely to cause the misfire? I'm sure I need new plug wires, they're original (180k miles), but anything else?
BTW, anyone who's never changed the plugs in a 4.6, be sure to blow the spark plug wells out before you remove the plugs, they can get a LOT of dirt in them, especially if you live in the desert. (My left side had a lot of oil in the first two also, from me being sloppy when I had added oil).