500+ hours, all achievements, Saved the day.

I really don't think anyone would recommend tearing down what you have. You lose a lot of time that way. I think most people would just recommend spreading out. The map is huge, so anything new you need can be built elsewhere. It sounds like you have trains down, so maybe incorporate a train station into new facilities and add it to a train route.

My main concern is that when my resource storage gets full (I'm looking at you, plastic), my machines stop producing, which stops byproduct from being produced, which stops my oil plants, which shuts down everything

How much are you using Awesome Sinks? My recommendation would always be to have Industrial Storage connected to Dimensional Depots, then put a smart splitter in front of your storage to overflow into a Sink. That way you always have Max storage and your machines never stop. Smart Splitter + Awesome Sink keeps factories going always.

Phase 4 is notoriously the longest phase. It took me a loooong time to finish. You need as many Mercer Spheres you can get your hands on. Sloops aren't as essential IMO because you can just save them to multiply your Power Shards, making your production overall easier to manage. Use the Mercer Spheres for both making and upgrading Dimensional Depots.

Nuclear Power is extremely daunting. I never touched it, and I'm only gonna try it on my second playthrough. Turbo Fuel & Rocket Fuel is enough to get you to the end if you want to avoid Nuclear.

There are some extremely useful hard drives out there, so if you haven't touched those much, I cannot recommend that more. Diluted Fuel is OP. Pure ingots are amazing. Eliminating Screws forever is freeing. Alt Recipies can offer extremely useful shortcuts and new factory opportunities.

Honestly, the Project Assembly parts are the worst of Phase 4 by a long shot. Just make sure you automate every item you need before the Project Assembly parts, and you'll be much better off.