[Tomvw]

It appears that you have wired the trunk lid incorrectly.
Check for short, to ground or another wire.
Check that all wires are connected to the right places.
Any of these could cause all of the new problems you have.

Unless the key is turning more than 90 degrees in the door, I expect it would function correctly.
Note: It takes a bit more force on the key in the door, if the central locking system is not working.

 

[Tomvw]

After you get the trunk lid problem corrected, you might like to address the old problems.
Seems like there is water leaking in under the carpet, this is likely coming from from the door.
Ensure that the inner (metal) panel is properly sealed and not leaking. (There can be a lot of water under the carpet before you notice any dampness on the surface)
Do a scan of the CCM and post the Codes.

It looks like you have a problem with the floor harnesses or grounds or the CCM, you can get this fault with or without water ingress.
Locate and fix source of water ingress, if any.
I suggest you completely unwrap all of the CCM harness and pull the wires apart to find the splices, any corroded splices need
to be cut back, soldered, and covered with marine grade heat shrink tubing. (You might need to add short wires to replace what you cut out)
Also check ground connections (1 on floor and on "A" Pillar), and check CCM/TCM and "A" Pillar connectors.

Have a good look at this link, before you start.

Passat Comfort Control Module - harness repair.docx

Shared with Dropbox

www.dropbox.com

This thread attempts to bring together all the problems regarding water ingress and their solutions.
Water Ingress and Solutions

 

[Tomvw]

You should fix the trunk lid first. Or you won't be able to do a scan.

 

[Tomvw]

I have tried my best to fix the trunk lid in anyway I can, I have checked the cable connections dozen of times, everything is connected and in place. I just don't know what else to do. I did forgot to mention after installing all the stuff I pressed the trunk hatch, and i noticed something, the number plate lights came on, I heard a noise from the latch engine and the clock and the trip meter got reset. After that nothing worked at all, fob key, windows, no radio signal, dome lights etc.

It appears that you have some of the trunk lid wiring incorrect. Maybe a wire that should go to the lock motor connected to the NP lights. You need to carefully check all wiring in the trunk lid, and match wire colours to their correct locations.
Then check fuses #6, #14, & #38.
While this situation exists, you will not be able to scan or fix the CCM problems.

 

[Tomvw]

Anyways after lifting the carpet to uncover the CCM box I noticed this ground cable, you can see the pictures that it is indeed very corroded. What do you guys say about this ground cable? Would it be functional with this much corrosion? Is this my problem? I have yet to check the A pillar.

No sign of water ingress or leak at all. Everything was really dry, carpet showed no signs of water damage or mold, the box was like new, it even smelled new when I opened it.
So signs of spliced or bad cables except this ground one.

I tried to scan with my aftermarket OBD-II scanner. It seems I cant scan the CCM at all. I get a "Cant communicate" message.

In post #9, I told you that you would not be able to scan the CCM.

After you get the boot lid sorted, do the following:
The ground might be part of the problem.
That ground connection must be completely dismantled, thoroughly cleaned, and reassembled with dielectric grease.
There has been water ingress. There are splices in the CCM wiring harness, you need to find and check them.
You should check the CCM PCB for corrosion and cracks, also check the pins in the connectors.
Then scan and post the codes.

Note: The incorrect wiring might have damaged something.

I suggest you disconnect the battery NOW, and leave it disconnected until you have completed the instructions in the post above and this post.