Yes, it is possible to bypass the ISO connector altogether. I haven't confirmed the pin numbers with your email, but assuming you got them from the diagram, it should be good.

I don't recommend doing this, as it makes life hard if you ever want to resell the sled or add features later.

The larger pins go for the larger holes on the dock, the ones for constant power and ground. If you look at the diagram you can see which ones are the big ones.

You should use the same gauge of wire as you would find in most standard car stereo installations. Nothing special. I don't know what gauge that is, but I remember the wire thicknesses on my sleds being the same as you would find on other car stereo installations. Go a little thicker on the ground wire and constant power wire just to be on the safe side.