So you're using some weird definition of "skinner box" where you simply mean "human inputs lead to various outputs". Why use this definition? By this definition a fucking mathematical function is a skinner box.
I simply do not understand, in general, what you're trying to say.
You should, if all goes well, be able to win. I'd look for a defense drone, I'd upgrade shields to at least 3 bubbles (I know you have the Zoltan shield, that helps, but still, for the flagship you're going to want more shields), and I'd maybe swap out a beam for a pew-pew if you can find a decent one. Or upgrade your hacking. That works too. And sell some stuff. I'd sell both the system repair and the anti-drone, but that's just because I find the anti-drone downright useless. Sell one of your missiles, probably the breach, and sell a beam, you absolutely don't need 3 of them. With that cash you can buy some upgrades, I would prioritize hacking and oxygen. A helm upgrade also wouldn't hurt, but only do that if you have the cash for it, I wouldn't make it a priority!