How do I go about a redesign?

So I've been using the same factory with little removal of anything for this entire playthrough but now I'm working on Phase 4 and struggling with constantly running out of storage and not being able to route materials to where they need to go. At this point I really think I'm going to need to level my beginning factory and start from scratch, how would you recommend going about it so that I don't accidently make it worse?+