2015 Fusion 1.5L Wiring Problems

[Araboy]

I have been struggling with multiple issues over the last few months and each time I've tried to fix the issue, another pops up.

 

Vehicle is a 2015 Fusion SE 1.5L without heated/cooled seats and without push button start.

 

ISSUE 1

Started with a severed bundle of wires (image with TOP VIEW shows this issue) in the lower engine compartment on the front driver's side. The car wouldn't start and it said there was a problem with the parking sensors. The gear selector on the dash did not indicate that anything was engaged.

The wires were part of the gear shift select/neutral safety system that allowed the car to start because it knew it was in P or N.

I spliced the wires together and everything was fine. For a while...

 

ISSUE 2

Started with my radio shutting off to conserve power and my dash lights went out. They came back on and turned off again several times. Until I shut it down and turned it back on, I couldn't get my speed over 35 mph even with the pedal to the floor. After shutting down, power returned and I drove to a garage to have them test the alternator and battery. Testing indicated both were fine. When I started it to leave, dash lights went out and I couldn't put it in gear. Shut it down, started it up, and everything was fine. Then "Charging System Service Now" message popped up and came up every time I drove it.

Tried to replace the alternator but the message returned.

Pulled the driver's side bumper off and found that there were some crushed and exposed wires on a large wiring harness. Image with "2" shows this issue. Clipped out bad sections of wire and spliced/soldered them together and taped them up. Everything was good again.

The picture of the full harness marks the locations (I'm 99% sure about #1 and 100% about #2) of the two wiring problems. The harness is for the starting/battery/charging system.

 

While working on the second issue, I found that there was some crust around the water pump seal and the wiring below it was wet from seepage. Coolant wasn't really low but I am going to get the pump and timing belt+tensioner replaced before the water pump fails.

 

This morning, I started the car to head to work and the orange wrench came on indicating a general powertrain fault. I have Torque Pro and didn't get any codes. I left the car in my driveway and took a different one to work. Is the wiring feeding that system part of the same harness? Could the fault be related to the water pump? Seems hard to believe that my luck could be so bad that this is coincidental and unrelated to the other issues. 

 

I was going to try to tackle the water pump and timing belt myself. I have the factory tool set and parts but I am concerned that I will run into an issue and be stuck. 

 

Any idea what it costs to replace the water pump and timing belt? I was quoted $1500 by my local Ford dealer but that seems ridiculous for about $300 in parts. I know it's not the simplest process but a good Ford tech could probably do the job in a couple of hours, right?