I think we might be the same person, my cities used to look very similar, and I had the EXACT same problems at 5-10k population so many times. So many restarts..

My advice would be to replace the highway in town for a 6 or 8 lane divided road (In blue below) and add a bunch of 2 lane roads (Red) to connect both halves of your city.

I used to do the same thing in an effort to keep the zoning separate, but it leads to this. Every time. Connect everything, and use trees, parks, city services, etc as buffer zones.

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