During start up I am getting knocking noise..

What are you talking about? OP has a gen 3, brought his gen 3 to his dealer, and had some fixes done. That's the only thing that's clear, everything else stated is confusing and likely not reality.

I mean, nothing is clear we're just taking shots in the dark since OP disappeared right after posting. Did they do nothing while telling him they replaced the EGR "harness" and gave him a bigger EGR pipe? Did they replace the pipe with one that's bigger? Does that part even exist?? Did they make up an EGR recall?? I know dealerships are known to BS, but this level of con or incompetence would be hilarious. It reminds me of the time my kitchen sink was shooting water out of the drain, and the handyman told me the cause might be algae build-up in the spray hose.

 

I had a plumber tell me a 40 foot run from the hot water tank to the kitchen sink wouldn't cause me to use more hot water.

 

Higher octane in a motor that has compression that requires a lower octane will just create more carbon build up over time if I am not mistaken.