Update 2:

In Eddington, there exists two central industrial areas: 

1: Near old town. It's well connected and designed, with minimal traffic.

2. Surrounding the Port. It's, as one reddit user put it, "too well connected.' 

Before the rework:

After a reddit thread, several constructive comments, and many hours of trial and error later:

(The traffic in the lower-left corner self-regulates; it ebbs and flows with every train that arrives at the station)

What changed:

1. Removed one cargo port and freight station.
2. Removed direct connection between the ports and the rest of the industrial area.
3. Replaced major intersections with two-lane roundabouts.
4. Reworked the layouts of the industrial 'neighborhoods' so that there is one in and out connection each.
5. Moved the existing train stations away from the major arteries so that trucks bearing imports/exports don't clog traffic.
6. Removed industry that faced the major arteries.

So, the lesson learned:

When in doubt, use a roundabout.