Bryan,
I hate to tell you that I fought a case like this once.
I wish you luck as in my case the trailers main harness had taken a hit because of a manufacturing mistake that crushed the cable.
If you are measuring things with a meter, a bulb may look a lot like a short. Start by taking all the bulbs out. (When you go to put them back, clean things and use di-electric grease.)
Do you still have the shorts to ground that you had at the start?
If yes, you have a real problem. Inspect the harness for as much of its run as you can. If you can't find the damage, try to borrow a "cable tracker". If you attach this to one of the shorted wires and follow the cable route, you should a serious serious loss of signal where the short exists.
Be ready for a fight.....
Matt