I appreciate reading your story. I'm ~6 years out of school having been in large companies and am wondering if it's normal to have the joy sucked out like I'm experiencing. If you don't mind me asking, how did you end up finding the small startup job? When I look at the job boards they're often dominated by the big guns or it's hard to sort through lots of small (oftentimes shady) postings - I don't know where to go to find small-by-design companies or similar mindset jobs.
I wish I had a better answer but like in almost all cases, it ends up being your network. In my case, my brother-in-law had been working for a few years at the company and he knew the founders as a couple of them were his mentors in grad school. So I knew enough about the company and when they needed to hire someone, him being able to vouch for me was enough to get me an interview with them.
That being said, I think places like ziprecruiter / indeed will still have job postings from smaller companies. The challenge, as you mentioned, is trying to figure out the good ones from the sketchy/shitty ones. Small companies can also be challenging if the management isn't great and they have bad culture. So I would definitely place a lot of weight on that if I were interviewing at smaller companies.