I'm surprised to hear you're having balance issues, especially with the new non-skill system. It's a game, and it's not like you have to have a perfect solution. I had to repeat a segment an extra time or two due to a combination of my own goofs and just getting a measure of (and reduction to) various time/resource costs.
And because of the nature of the game, I feel that was effort well spent. If a later element is less of a struggle because I needed a few extra trips to Santorini, I feel vindicated, not robbed of... what, opportunity to struggle?
Make it work, make it fun... not just for us. You deserve to enjoy making the thing too. Don't go burning out on advanced calculations just because you think this point in the story should have us sweat out half our last water bottle. Plus, I think you've already solved that with some stages of the drilling draining water faster.
It's a cool playground you're building with text and menus. ^_^
The issue with balance is more along the lines of "ok, player just reached a new facility, and I want to give them X upgrade. I/my testers now need to check to see if getting that first instead of last trivialises the rest of the game." Or, to give a more recent example, I wanted to add an upgrade which fit with the story, and once you unlocked it, you could get it from the start of each loop. But I couldn't because I didn't know what effect it'd have on anything, and didn't have time to test.
This tool is specifically so that I can have fun, adding what I want when I want without having to stress about what it's doing to the game because I'll already know.
I really appreciate your message though, and don't worry - doing a different type of calculations for a while will be a nice break from hitting my head against bugs which don't want to be found :D