Standalone wiring harness for alh

I have completed most of the grunt work that comes with my engine swap. The most troubling factor left for me is the wiring harness. I've read many threads and decided to go with the less cluttered look of trying to narrow down the harness to the bare minimum while still being able to communicate via vcds.
First some background. The donor vehicle is a 1993 Toyota 4runner v6 and the engine that will go in it is a 2002 1.9 TDI from a manual Volkswagen bug. I've got a Malone stage 4 tune with an immobilizer and EGR delete I've also put on a vnt 17 turbo as well as upgraded injectors and map 3 bar sensor.
When I first hooked it up to vcds I could communicate with it just fine but was not able to start it. After I let it sit for a couple months I came back to it and can no longer communicate for whatever reason. But one thing new that was happening was that my relay 109 was clicking rapidly. Tried a bran new oem relay and the same thing happened.
I've taken some pics to help in the discussion of where I'm at. Can I get any conformation on weather the wiring harness is correct or not? Also any ideas as to the rapid clicking on relay 109?
Here is a pick of the half of the wiring harness that I delta with. The other half is unchanged.
Below are some closer look photos
This is a photo of my fuse box that I basically kept the 4 essential fusible connections from the original box and replaced it with a cleaner more compact one.


I will try and get some more photos up as soon as I figure out how.

Photos not working.
How is the 109 relay getting its power? How about the ECU?

I tried the upload photos to the gallery route. Is there a better method?
As for power, I have power sent to the main red wire on relay 109, pin 3 (via black/lilac) power to obd2 port, and the 2 main red power wires at the other end of the harness. I tripple checked my ground wires (unless there's some damage mid wire).

I didn't see an answer in the pictures, but someone else may pick up on something.

all of your grounds tied in ?

Most all grounds were grounded to the same spot. Could that create an issue?

I've uploaded a couple more images. Hope these may help identify a problem.

I found some time to look at my wiring issue again. I was able to re-communicate via vcds by just grounding the ecm. Has anyone else had a need to do this or could this be a possible sign of missing a ground somewhere or something?
With the ecu grounded I began trying to diagnose why I still am not getting it to start. It turns out I'm not building enough pressure to open the injectors. I would guess I'm getting approximately the same amount of pressure as my lift pump is producing (3-5 lbs). I'm leaning towards my injection pump being bad but does anyone else care to put in their two cents before I make the plunge to purchase a new pump?

The ECU case is internally connected to the ground wire in the harness. Since grounding the ECU makes things work it tells me you have a missing ground. Check the entire length of the harness and ground any brown wires you find that are not connected to anything. There should be one near the ECU.

As far as the pump goes, check for 12V at the cutoff solenoid while cranking. If there is no power there it won't deliver fuel under pressure, but it might dribble some out. When you turn the key on do you hear the QA cycle through its range?

^^what he said.

You have two brown wires with terminals on them in your posted pictures - those guys need to be grounded. No, it doesn't matter if they all ground to the same location...in the end it all ends up back at your negative terminal on your battery.

Don't condemn your IP until you're sure your wiring is providing the correct signals and you've properly bled the system.

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