I would advise using efficiency modules everywhere you don't use prod at first, until getting to space and getting a few more damage upgrades at least.
If you're doing core mining, use air filters around them as they spread a lot of pollution. Military control is hard at the beginning of the space age in SE because of the lack of upgrades so you'll have to either go big or reduce pollution IMO.
Bugs should not be attacking your railroads at all. If you're terribly unlucky a bug can get grazed by a train and then it turns hostile, but that should be pretty rare before behemoths.
Handling the production curve means having more ressources available. My advice would be to use nuclear power to run 6-8 core miners or more, enrich the ore you get from this, use vulcanite recipes in industrial furnaces, prod modules at every step of the production chain and make plenty of use from air filters to keep pollution under control.
In my completed SEK2 run I had a ground main bus with all types of circuits, coal, iron and copper plates, steel, stone, rare metals and all different kinds of petrol fluids. It worked very well. You don't really need to bus all the intermediaries.
One of SE's design decision is to let you unlock methods of doing things you were already doing more efficiently. Your production chains will change and you will need plenty of refactoring once you're in space. That's just how the mod is designed, almost everything you'll build in your first run will need to be redesigned at some point.