I don't see any reason to panic, and it's certainly not "too late" - nothing wrong with taking a gap year or two or more to build up your research portfolio and interests. I switched fields in my junior year and decided to take a gap year of full-time research for this reason. It was the best thing that could have happened to me, both as an applicant and a person.
I agree with your last point: seems like a lot of pre-meds have the impression that working in more than one lab simultaneously will be regarded more favorably than a single research position (ie. *I* thought that). I think that really only holds true in the unlikely case that you are very productive in both and end up with papers/other deliverables from both. The more likely outcome is you have "okay" results in both that reflect part-time commitments, which is nowhere near as good for your application as one very positive experience with a glowing LOR and completed projects. On the other hand, it sounds like you were in a weird situation with your other PI leaving the university, so maybe this is actually a good thing and you can now consolidate your research to one PI.