Hey guys I'm new to this forum so I thought I would contribute a possible fix for your misfiring problem in your 1999-2004 4.6. I started noticing a lag in the acceleration in my 2004 gt, especially when it was hot. After a few weeks of this, my check engine light finally came on. I got p0316, which is misfire under 1000 rpm. Not being specific to one cylinder, I cleaned my mass airflow sensor thinking that it may have been the problem. I started my it up on a cold engine, and thought I had solved my problems. Unfortunately, this was not the case. Next, I turned my attention to the ignition system. I thought that one of the coil on plugs was possibly malfunctioning. Finally I got a error code for cylinder number 5, so I immediately removed that coil. After testing it with an ohm meter, it seemed fine. When I was about to put it back in I noticed a crack in the rubber boot. Realizing that this could be the problem, I got a new boot from my local Ford dealer for 10$. I put it in and haven't had an issue since. As far as I can tell, the spark was intermittently escaping out of the crack instead of making it to the sparkplug. The hotter the rubber got, the easier it was for the spark to escape. Simple fix for a relatively common issue. Hope this helps