chasing electrical

My battery was dead and when I put a
different one in I didn't realize it was too tall
and closed the hood. The positive post
welded itself to the hood and some of the
wiring melted and burned through the
carpet. I had to rewire the fuel pump just to
get it running again and now I'm having tail
light and brake light issues. With the key off
when you press on the brakes all the
warning lights in the dash come on. When I
use the turn signal it's like I turned on the
hazards. When I turn on the lights all the
front lights work properly but the tail light
are messed up. The amber lights stay on
and the red lights are very dim.  Where do I
start ??