Tail lights all mixed up, backwards, and wrong.

I removed the truck bed to fix a fuel tank leak and
put some external trailer brake lights in the rear
connected by a 4 pronged adapter.
Everything worked good.  The lights were very very
bright.  Bulbs only.  Then I kept the headlights on
for a while which illuminated the rear ligjts too,
smelled a burning scent from behind or under the
dash, and now the lights are all messed up.
The break lights wont work even though the brake
switch works according to the ohm meter.  The
right turn signal activates the left blinking tail light.  
The left signal makes both rear lights blink fast
and dimly.  The emergency flashers work but the
right bulb is much brighter.  And turning the
headlights on causes only the left tail light to light
up.  I bought a new emergency flasher relay and it
still works the same.  The same external trailer
lights work perfect on another truck.  Hooking my
truck up to another trailer gives the same screwed
up results.
I checked every single fuse in the fuse box that is
inside the cab and the other fusebox thats under
the hood.  The relays in that fusebox dont effect
the rear lights.  Any ideas?  My truck bed is now off
the truck and i am searching the wiring everywhere
but have not found anything yet.