I did a couple of hours of work this afternoon, and i would prefer not to start over again. Hopefully you guys can help me out here and fix this so i don’t have to restart. 
Ok, because i have a JVC camera, i need to do this tutorial to make the files work with premiere. http://eturkov.blogspot.com/2008/05/working-with-mod-files-in-adobe.html
You will notice that one step is “Interpreting the footage” as premiere and after effects just think it’s 4:3, when in fact it is 16:9. That is easy enough if you remember at the beginning of your project, which luckily i had remembered for the Premiere file. I didnt for the after effects composition. After having the dynamic link workflow going all afternoon i have the movie at a place where i want it, but when i export using aftereffects, it has weird sidebars. http://img26.imageshack.us/img26/8527/snapshot20090420202655.jpg
Now, to try and fix this, i went to composition settings and reset it too D1/DV NTSC Widescreen, which the premiere file is. I went to “Interperet footage” and applied it to all the clips, then selected all of them and hit “reload”. nothing happened.
yes, i can just hand my movie project in like this, but i would really like to solve this problem, because it looks dumb, and will lose me marks.
thanks guys in advance 