I ran the wire from my roof basket to right between where the front and rear doors close at the top. Popped a small hole in the weather stripping then ran the wires under the stripping all the way down the door frame (inside the weather stripping - it pulls back very easily) to a point across from the fuse box, then under the hinge and over to the fuse box where I connected it. The doors close with no problem. The wire doesn't pinch anyplace and I didn't have to take anything apart! You could simply put a connector at the top where the wire comes out of the weather stripping and you wouldn't have to do any drilling or anything to the roof. When the doors are closed, you really don't even see the wire when the basket is in place. With it off you could tuck the wire connector inside the door top where it would be hidden. There is plenty of air gap between the top edge of the door and the weather stripping to tuck the unused connector when the basket is off.
My wire looks thicker and bulkier than yours would because I have my wiring inside split loom which really wasn't needed but I originally thought I would need the abrasion protection where the doors closed on the wire. Turned out the way the wires are run between the doors there is really nothing rubbing on the wires. At some point (like that will ever happen!) I intend to remove the split loom and replace the wires with a heavier guage of 2 conductor wire instead of the 2 individual thinner guage wires I have now. It will look neater coming out of the top.

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My pics!!'03 Rennie w/all Tupperware
Custom Roof Basket
Mopar Tubular Brush Guard
Garmin GPS V & Laptop w/Nav software
RAM products laptop mount
Maglite w/mount
Rear cargo bay tool cabinet
AllJs Rear Shelf
Rear receiver
250k miles!
LOST #CR051230