Alright, wow. That sucked. But fulfilling too... old lower harness is out and new one is in!
I have taken some pictures and this is not a professional write up, but I hope it can help anyone doing this job (if I even did it right).
I did it all with a ratchet set (large and small ratchet with 6 and 3 inch extender bars), small screwdriver, large pliers, shoelace and 1 or 2 wrenches. Here's what happened and where I'm at now:
1. (Battery unplugged) I detached the connections to the lower wire harness in the engine bay, behind the firewall on the passenger's side. After working them through the opening in the firewall, there is a metal clip that had to be unscrewed before the harness was free on the top side.
2. I unscrewed the nuts attaching the harness to the alternator, the smaller screw is a pain in the arse, but I managed it with a socket, held in place with my finger and turned with a pair of pliers:
3. Moving on to the starter. I removed the three bolts on the starter heat shield. The two on the back I removed with a ratchet and I believe the one on the front I did with a wrench. It was also a pain in the arse. (No pictures of this step).
4. I then removed the large nut and small screw attaching the two wires to the starter. (No pictures, but pretty straight forward).
5. Next, there is a large nut attaching a metal clip on the harness, as well as the dipstick tube. I had a 6 inch extender bar on my ratchet and it was
TOO LONG. There was not enough space between the nut and another heat shield to properly line up the ratchet. After searching hardware stores for a slightly shorter one to no avail, I tried again with a very large amount of elbow grease. I managed to jam the ratchet (not recommended) against the (flexible) heat shield and barely made enough room to loosen the nut. This took
a lot of strength and upward pressure. To anyone reading this, please have the right size extension (5 inches?).
6. With the clip/dipstick nut off, the harness was now free, or so I thought. I pulled and pulled and tweaked and tweaked and worked the harness from all angles. There was no way in hell it was coming out. I would have been comfortable hanging on to that harness, off the bottom of the car, half way off a cliff, with velociraptors gnashing below. It wasn't coming out. I then decided to loosen the dipstick tube. There is a bolt that I removed with the small ratchet and 3 inch extension.
This bolt is located behind the horizontal pipe and in front of the vertical dipstick tube, on top of the transmission pan. You have to feel for it. I unscrewed it very slowly, expecting trans fluid to spray out, but I got the bolt off with not so much as a drip! I gently wiggled the dipstick tube and had a couple inches play, hopefully enough to remove the harness. I then got to work on wriggling and yanking the harness out and noticed some warm red liquid on my arms. OMG it was blood everywhere... and then a severed hand still attached to the forearm fell on my shoulder!!!
AAAAAHHHHHHRRGh!!!!
Oh wait no, it was transmission fluid, even worse. I ran a got a pan to catch the fluid and found that the dipstick tube was completely free and then I yanked that harness out so fast.

7. After cleaning up, I installed the connections on the new harness to the alternator and starter. The section where the harness travels from the starter to the alternator has some metal that the old harness was rubbing against. It caused the old harness to wear, almost in half. Here is a picture of that area with the harness removed. The section I am referring to is the pale yellowish metal, second up from the bottom in the picture:
Here is a picture from the alternator side, with the new harness installed. The new harness has a flexible, ridged plastic covering (like a bendy straw) to prevent it from touching the metal. (The old harness did not have this).
8. I then fed a shoelace down beside the dipstick tube in the engine bay (tied to a rail). I attached the shoelace to the harness and pulled the harness up top into the engine bay.
9. I re-attached the dipstick tube and attached the metal harness clip. I think the orientation of this clip is important. With the metal tab facing inwards (towards the front of the car), it makes it so that the harness is not touching anything (heat shields everywhere).
10. I then routed the new harness through the firewall and attached the connections. I went back and made sure all connections were secure and the heat shield re-installed. Done! Here is a picture of the new and old harnesses and the area of wear on the old one:
11. With the battery attached and the car ready to fire up, I turned the key in the ignition aaaannd! Nada. The exact same symptoms. The power works fine, but as soon as the ignition is turned there is a loud pop/click and the car does not fire up (see previously posted video). The exciting news is that I have a new noise. It's a light, high pitched whine. It's coming from the engine bay with the key in, even when the driver's door is shut. Any ideas about the noise? I'm assuming my starter is fried?