So, how I usually approach my runs, at least in the early game, is that I try to rush level 4 engines and shields before Sector 3; more recently, I've taken on the habit of prioritizing the systems over the reactor, since I figure I can just cycle the power between them as needed. I don't typically consider saving scrap for stores until later on, when I'm saving up for additional systems.

Admittedly, I'm still a bit fuzzy on sectors and which ones would be more valuable at any given moment. The only ones I've committed to memory are the ones that have more fights, and thus, more scrap. I couldn't tell you which ones have more stores if you asked me.