You might try using a jumper from a known-12v (like the battery pos!) to the wires in question... if they light up, the "continuity" or resistance is what is normal. If it sparks and blows a fuse, well, then you have a short!
Gee, while that sounds fun, I don't have any lights connected yet. All lights were removed to be replaced with after-market ones eventually. Anyway, I am sure my problem is impossible to diagnose over the internets... hopefully if I keep staring at it for another 48 hours just as I have been for the last 4 hours, it will fix itself!