Sorry for the late update. But I have fixed it, the rattles at least.
Like I said before I went ahead and got the dynamat door kit and at first didn't think it would work after doing just one layer on the passenger door. Keep in mind this is the door I have been working with and had maybe slightly more rattles then the driver. So after dynamat and a rolled up shirt tightly placed in the map pocket didn't work I decided to get a sheet of fabric/carpet like stuff and cut it to place in the door as well just to give it an extra layer. That didn't end up working, just to hard to cut perfectly and get placed right. So I also tried porting the sub enclosure like candyredcs suggested, and I really thought this idea would work as I thought the air inside the enclosure was just being pressured too much by the sub. But that does not work, DO NOT TRY AND PORT THE SUB ENCLOSURE, it just allows the sub to vibrate more plus the tight bass you get by keeping it sealed sounds so good!
Now I am having problems getting the enclosure on the passenger door back attached and sealed to the door. As I said originally I split just to see if something inside was vibrating. It's not, here I go again DO NOT SPLIT THE SUB ENCLOSURE, whatever ford used to seal it is the real deal. I have tried everything up to 3m semi rigid plastic repair to put it back together which cost a little more than $100 for the gun and everything you need to use it. It didn't not work and now the door is at a body shop being repaired.
Now on to what worked to fix the vibrations, first of all the main thing is just a lot of dynamat. I have 3 layers on the outside of the sub enclosure, and then at least two layers all around it and one on other parts of the door. The stuff is expensive but to me it's totally worth it. I'm probably going to get about 30 more sq feet on eBay, it's pretty cheap there (more than half price compared to places like best buy or crutchfield), to do the rest of my passenger door and trunk and wherever else. I also got about 3 feet of Velcro and used just the soft part of it to do things like the window control panel and I even unscrewed the door handle from the back of the door and velcroed it along with the back of the ambient light module. Now I'm not sure that was 100% necessary as it required breaking part of the door handle assembly to get it out, so if you think your handle is vibrating take caution when going to take it out. Now the last part is I took some stiff foam I found at lowes and used carpet tape to adhere 4 layers ( about 1/2"-3/4" wide) on the backside of the sub enclosure to brace it as best I could. I also still used the t shirt in the map pocket to remove those last tiny rattles.
When all said and done I am very happy with it especially considering my new amp gives these subs right at about 180 watts which is 6 times more than the stock amp provided. If anybody has any questions on how I did certain things please feel free to ask. I will be uploading pictures soon of my project.