The stock looming is really quite over-sized in almost all areas of the engine harness. Once you unwrap everything and clean it up you can cut the girth of the harness practically in half in most cases. In the areas you circled I believe I used 3/8" TechFlex F6. It was either 3/8" or 1/4", I can't recall exactly.
If you look closely you can see a little of the harness on the driver's side in this picture of my engine bay...