Great that helps alot in case anybody is wondering it goes like this
Blue/Red = Running lights
Green= Left Turn
I may have the turns backwards I have some more testing to do. I also discovered fuse #1 by the pasenger side of the console panel was blown, that is why none of it would work at all with all of my testing.
The original problem is still there though, it seems the brake lights and the flashers work fine, but the turn signal will flash both lights instead of one or the other. Also the running lights at night will not come on (this is all in the trailor only). I am noticing that one of the bulbs on the trailers may be out, could this cause this problem? Also the Red/Black wire was completely rotted through with bluish green corrosive, I presently have it going no where, on the diagram it has it listed as "Fused B(+)", should I have it crossed over with another wire?
I have gone through the rest of the fuses they look fine, as long as I have got it this far I can tow during the day and use hand signals. But it would be nice to be able to tow at night as well. This is kind of confusing, I am use to running everything off of the tail lights, but it looks like the Cherokees don't work that way (sucks to diagnose).