Brake lights will not work except for the third light that is on the trunk, I have taken it to the shop they said it was the harness but that did not work. The only other thing I can think of is the multifunction switch needs to be replaced, any advice is appreciated.

 

That's a pretty garbage shop... hopefully they at least gave you some kind of refund.

Before throwing more parts at it, I'd break out the multimeter and wiring diagram and figure out what exactly has failed (which is what the shop should've done in the first place). I agree the turn signal switch is the likely next step (its a very common failure point om the 5th gens), but it only takes a couple minutes with a meter to 100% confirm.