I ran my wires from inside the driver's footwell, into the door jamb, by just sliding them under the trim piece seen in
this photo on another thread. Actually, that is not correct. I moved that piece to gain access, but actually ran it under the rubber seals that are just outside that piece, and in the jamb itself. The piece he is pointing at with his magnetic wand is where I am talking about. Then, if you look forward, inside that door jamb, towards the top, there is a vertical hole, about 1" long and 1/4" wide. I inserted a wire stick/pull into that hole and worked my way up under the hood trim (which you need to remove). I last did this 3 years ago, and did this on 3 different MS's, sometimes easily, and sometimes it took a few tries. I think once I stuck an LED light on the end so I could find it. I also ran an extra wire, in case I ever needed to pull another cable.
You will have some wires minimallyexposed in the door jamb, but they lay flat and never caused me any issues.