So a few things:
You have two years of two languages if I’m reading correctly. But that doesn’t work: Three to four years of one world language (ancient or modern) taken during high school.
I will say that’s not necessarily an eliminator but it might be. My daughter got into a very selective LAC (not Columbia selective) with two years in one language but the school cancelled the third year over summer and the counselor noted this.
Science - did you just have two? You said 3 credits - do you mean 3 other classes? Were they lab sciences?
Have you checked the NPCs of all the schools you are looking at - for example, Syracuse, etc.
I wouldn’t take the ACT again.
I would say no to Columbia - but if there’s a portfolio involved, you never know.
It’s highly rejective - so keep that in mind. And you are rural, that will help. Transgender - I don’t believe helps.