Well, I finally have all of this resolved. It's not easy when I'm just waiting on my brother to do the work, because I refuse to pay a shop when my brother does better work (most of the time).
I have gone though and done a few things that has resolved the smell issue I've been having. Pics to follow.
1) There was a large exhaust leak at the first flange on the Rawtek DP/DPF delete. It was hard to see, but when I finally got my bro to take it all apart, here is what we found:
2) The EGR pipe coming right off the turbo was leaking right after the flange that bolts to the turbo (that's a high pressure leak causing boost surging).
I bought a new pipe and then brought it to a local fab shop and had a custom EGR block off plate made. I already have the Darkside EGR block off installed on the cool side of the EGR cooler.
Now I have it blocked off right at the turbo.
All of the exhaust leaks are sorted, and the EGR cooler has been plugged and is just sitting there doing nothing. I thought about trying to delete it all, but I wasn't about to ask my brother to open that can of worms.
3) The cowl! The cowl/scuttle never really wanted to reinstall and settle correctly. So A few screws were added to seal it,
but you could still see light shining through the cracks when searching. Terrible fix, but honestly, it worked great and was cheap, we just spray foamed lightly from the inside. It worked, I know its not proper, but don't hate too much.
Other changes... for fun I added a magnaflow 3" exhaust. It looks decent and sound decent. A bit meaner and more like a performance exhaust than a straight pipe. I'll get sound videos when it's not raining here in NY.
I've also installed 17.5mm spacers in the front and 25mm in the back. It looks WAY better.
So, my issues are all good now, it runs and drives great. It also doesn't smell anymore. I'm very relieved. The wife is happy and that's what matters.