I got mine done. I used the Kenwood KFC-6982IE 6x9's with baffles (so the magnetic isn't touching the roof of the truck). I decided to leave the 4x11 hole as is, and mount the 6x9 speaker from the topside. I thought that if I cut a hole to expose the whole 6x9, there would not be enough beef left in the bracket. It was an M-F tight fit but it works, and sounds great. So, all I did was:
1) removed the bracket (with speaker) by removing the 2 bolts accessible under the headliner, and pulling the bracket + speaker out from under headliner.
2) Unscrewed the old 4x11 from the bracket
3) Drilled new holes in the bracket for the 6x9. Made sure to center the template guide so that the 6x9 tweeter would stick out close to center of the hole as possible.
4) Bolted the 6x9 to the top of the bracket
5) Squeezed the bracket with the attached speaker under the headliner and into position
6) On both brackets, on the bolt that is closest to the center of the truck, you might need a longer bolt to re-attach bracket. Or, you could probably bend the bracket up to use the original screws.
Yea, the 4x11 mount hole covers some of new speaker, but it still sounds WAAAAAY better sounding than the crappy 4x11's I used to have.