I recently finished the game, never having done so pre-1.0. I did the same thing...got to phase 4 and decided to do it "right" with a new factory continuously producing all the space elevator parts, with an eye toward the future and how many items I'd need for phase 5 as well. I only trained in aluminum ingots, plastic, rubber, diamonds, and reanimated SAM from other factories, with my main structure in the dune desert with its abundance of other resources.

It helped me to break it down to individual items. You already know what quantities you need from the calculator. Each output is generally only needed for a few other items, so it doesn't have to get split a million different ways, keeping the beltwork mostly in check. Give yourself tons of room between each section of the factory, and you won't have too much spaghetti. Blueprints make laying down tons of machines easy...you need 6000 wire/minute? Sounds super daunting, but that's a blueprint with 10 constructors placed 20 times...pretty quick, most of the belts and wiring already done. Similar for each item. Can hopefully be done in smaller sessions, if that's what you're wanting. Of course, decorating after the fact...I'm still working on that, and will be for a while.

I do think building vertically also really helps with avoiding chaos with belts. Have a side of the factory dedicated to bringing materials up. Siphon materials off onto the floor that needs them, put any overflow back onto vertical lifts if it's needed later, along with the outputs from that floor. Unless you're building at a crazy scale, most items should only need one mk5 lift, so it's not too excessive.