Bad Mod

If its a misfire it should have a code (OBDII)

This will likely get moved to the "Other Auto Tech" forum.

They sell a nifty little testing tool at places like Checker Auto and Autozone that plugs in-line between your plug wire/coil-on-plug boot and the spark plug, itself. It's basically a little light that just shows whether or not that plug is actually getting spark to it, without having to run the motor with the plug removed and laying on the block (the old-school method, more useful for no-start conditions than for drivability troubleshooting). Might look into one of those for around $15 to tell you whether or not you're getting spark to each of your plugs.

Usually on most OBD-II cars, you'll get a code thrown if there's any kind of a misfire, and it'll even tell you which cylinder is having problems (unless you just get a "multiple cylinder misfire" code). Even if the "Check Engine" light isn't on, there might still be some stored codes that you can pull. Did you actually check the codes, or is it just not tripping the "Check Engine" light?

Also, you can always start pulling the spark plugs you just put in and comparing their appearances. If you've got one with a whole lot of deposits on it, notably more than the others, that's likely your problem cylinder. What types of deposits it has on it can point to a whole variety of different problems.

with my 99 lightning it never threw a code. Also the one that normally goes bad is the pass side back one. you can have ford test them for 90 bucks and then replace it yourself costing a total of 110 dollars. I have a little tool to check the coil that I bought for 70 bucks but my problem was that it never missed at idle only at wot. Also you can check the resistance on them to check them. If you check out svtperformance.com and go to 2nd gen lightnings they will help you out.

Are you sure your not hitting the rev limiter Since it only does it at WOT

I would check with you local Ford dealer as there are new programming flashes very often. There may be one that will fix your problem.