I’m not sure what my research questions are
You probably do have them, they were just never written down clearly. To find them, it helps to first understand what research questions are supposed to do in a paper.
What are research questions supposed to do?
The research questions (or study aims) set the expectations for your reader: this is what we’re going to study, these are the questions we’re going to answer.
You state them in the last paragraph of the Introduction, and from then on your reader or reviewer, consciously or not, is looking for the answers in your paper.
Finding your research questions
First of all, have a look at your data, your results. You collected those for a reason. Why?
Why did you collect this data? What did you need it for?
This isn’t about why you chose that field site, those variables or that sample size. That’s the justification for your methods, and it belongs in the Methods section. The question here is what you were trying to find out by collecting it.
Sit down with it for a bit. Write it out, or better even, talk it through with someone. Your answer will probably take a shape like:
We collected this because we wanted to find out how X works.
We collected this because we wanted to know what X looks like.
Those are your research questions, phrased as statements. Turn them around and you have the question.
How does X work?
What does X look like?