What should I do if I'm trying to go into academic from a mostly non-academic background?
Generally, I do not believe that it will be problem that you do not have an extensive Master thesis. Most universities are likely to pay more attention to your grades and other documents such as letters of recommendation, motivation letters, etc.
So, the letters of recommendation could be a problem. I would advise reaching out to your old professors and tutors. Focus on those from whom you received good grades, briefly explain your reasons for reaching out now (in 1 or 2 sentences), and mention that you got a good grade in their course. At least in my experience, most professors/tutors will be willing to help. If it puts you in an uneasy position in your current job, then you should not ask your manager a letter of recommendation. This can easily backfire. However, it does not have to be your manager writing the letter. If possible try a more senior colleague whom you can trust.
If you apply for a Ph.D. position that is associated with a specific project, then make sure that you do your homework on the topic and show it in any application letter or motivation letter. The same holds for any position that associated a specific advisor from the beginning. In this make sure you know the advisor's work and research agenda.
If you feel not ready for a Ph.D. you could also consider programs that include coursework in the first year. Overall, do not overthink it, and do not forget that a Ph.D. program is there to teach you how to do research. In your application focus on conveying that you are able and willing to learn how to do that. Your professional experience could be a plus and more important than the perceived quality of your Master Thesis.