No Brake Lights

I am dealing with my son's 99 mustang, 5 speed, 3.8L. I noticed about a month ago while he home on leave that his brake lights were not working, even the third brake is out. Everything else works. I have read probably every thread in here and other sights at least twice pertaining to brake light problems but none seem to match it. I have checked all fuses and light bulbs, changed the multifunction switch, and made sure the brake light switch at the pedal is working. I have tried to run a bypass wire from the brake light. This works except now the third brake light flashes when I turn the left signal on and the brake light overrides the turn signal if I use them while the signal is on. I'm usually pretty good at rigging things up to get them to work but this one has got me stumped and it doesn't look like I am going to be able to rig it this time. Has anyone ever encountered this? I would be really grateful to anyone who could help with this. Thanks.

I have already tested the brake pedal switch and it IS working, as I hooked up a bypass wire and put a test light to it and the light goes on and off when I hit the pedal. I also tested it right at the switch and it works as well. There is also power in fuse 41. The grounds in the trunk may be a possibility. The only one I know of is on the left side new the trunk hinge and it looked OK anyway. Are there any more? I also noticed there is some kind of module near that ground. Any idea what that is for?