Hello. I've encountered some issues with my engine and need advice on how to systematically address the situation. I own two 1.4 TDCI Fusions; this issue concerns the older 2003 model. I don't recall the exact model level, but it's definitely not the base spec.

The clutch and the DMF flywheel were replaced by a very affordable repair shop. They mentioned they took a shortcut, which may have involved stretching the wiring harness. Additionally, the car had serious oil leaks from multiple locations, and the smell of exhaust gas inside was worsening progressively, to the point where I could no longer drive with the windows fully open. The repair shop did not want to address the exhaust gas issue at that time, and it clearly was a separate problem since it had been present when I bought the car

I watched some videos and successfully replaced the injector copper gaskets, though the process involved removing a 1-inch thick layer of black soot at its worst. During this, I accidentally broke the EGR pipe, which I then replaced. I also changed the valve cover, but later discovered that there are two versions for this engine, and I likely installed the wrong one. The exhaust became problematic when driving in traffic. I attempted to replace the injectors with used ones without reprogramming them, lost the correct order, and as a result, the exhaust turned extremely black. I then replaced the turbo, drove a few miles, received an EAC fail message, and drove home in limp mode. Since then, the car hasn’t started. At some point, I also broke the dipstick, and part of it may be at the bottom of the oil pan. There have been multiple EAC fails previously, which were likely associated with a broken or leaking EGR pipe and the injector gaskets. My ancient code reader was unable to read any errors.

Now, the car won’t start. I removed the battery box to seek advice on repairing the starter in my newer Fusion but ended up breaking three of the four bolts inside the threads. I drilled the holes, yet I can’t generate enough power with the extractor to remove the remains of the bolts. In the process, I noticed that one of the ECU connectors was broken; the locking mechanism was missing, and a piece was broken off the connector on the ECU side. There was also a small dent in the back of the ECU.

I know I probably have broken  a hundred "don't repair it that way" rules while driving that car, but I needed a car for my newspaper delivery job. Now I have more time and I would like to see, if the car is recoverable. My main issue now is figuring out how to systematically fix this mess. Any ideas on how to proceed?

In my mind, there is a confusion (pun, get it?) between the two cars.
One is working and the other not and you want info on the one that won't currently start?

Will it crank, is it firing at all, did it start previously has anything happened since it last started, what is EAC? (not in my brain cell yet)
You'll need to get it cranking and perhaps consider Forscan and a lead to update your scan tool and get some fault codes then live data to investigate.

The uncalibrated injectors are a worry (Forscan can do that)

All the potential breakages are an issue and suggest they are checked and kept in mind during any diagnosis.
My best guess based on my interpretation of your post.

5 hours ago, Shearers said:

what is EAC?

Electronic Accelerator Control (EAC) system

possible issue is that the two signals (two position sensors)are not agreeing with each other. It's designed as a fail safe system.