Thanks.
The 1st and 2nd non SR5 models didn't have the extra trim on the upper section of the panel, and some of the DLX's didn't either so I didn't have to worry about that for those panels. However I have repaired the upper section panel on friends doors. When re-covering the original panel I left enough material so I could fold over the top edge of the door. I then glued(using liquid nails, you could use contact cement after sanding the paint a little) the upper section to the door. Once the glue dried I cut out the areas(of the vinyl) that the oem weather strips pop into.
If you don't want togo through the extra work, you could also just repaint that section and just go w/the non SR5 style panels.