Ok I have sourced an uncut harness and put them side by side with my hacked harness. I believe I have everything hooked back up as it should be. I would like some clarification if you all don't mind. These are all under the dash of the passenger side of my 93 YJ, at the furthest end of the harness.
I found a diagram of dash wiring floating around here somewhere but it didn't really match mine.
I also understand there are going to be several plugs that will not be used from options that my jeep doesn't have. (AC, hard top, etc).
The speaker plugs are confusing to me, as I have looked on and spoke with METRA regarding their harness adapters and none look like they will fit.
All the wires i'm working with
starting from the closest to the fuse box (in this picture) and moving out towards the passenger side.
above and below are the same connector, just diff angles
further down this "arm of wires is this connector"
above and below are same connector, diff angles
I believe this one goes to the vent box, sticks straight into the connectors sticking out of the face of the box
and this one goes on top of the blower (hope i'm getting the names correct
I believe I have these two plugged in correctly as demonstrated in this photo
and these are at the furthest end of the harness