To directly answer our OPs concern: Yes, I think your 1st quarter grades will seriously impact your competitiveness. There is only so much you can do to average up a D, D, and F. However, it is certainly not the end of the world, nor it is the end of ultimately getting an appointment, depending on many other factors. We don't know your school's profile. We don't know the "quality" of the 3.6 GPA you posted earlier (ie, grades in key core classes), and we don't know the rest of your package, esp. teacher recs/SOEs and essays, CFA, medical status. I hope you did follow through and get your Eagle Scout and the CAP achievements. I commend you on those! Hopefully you were able to take the SAT/ACT and have a confirming solid score in those.
Pivot and reflect on your grades - it is not just the grades, but also your comment about "spend all my time on USAFA application". This year, as much or more than any other, is to see who THRIVES and who wilts in the Covid environment. This answers the question - does this candidate have the demonstrated capacity to THRIVE at USAFA (in this new world environment)?
Class of 2024 has one of the highest AFT scores (I think during Basic), and after midterm exams, has one of the highest GPAs in many years. What does this tell you? That the Cadets selected are able to THRIVE in an uncertain environment, fluid and ever changing rules, and actually extra competitiveness in dealing with Getting Stuff, Getting Stuff Done, and Thriving With Limited Opportunities (e, clubs have reduced spots or not able to operate due to Covid), and at any time BOOM! you could be in Q&I, disrupting all other plans.
Clearly whatever you did (or did not do) 1st quarter must be corrected. The best thing you can is reflect on why - an F is really bad. I mean, it's an F! A D could be explained, but it's still a D. And you got 2! Is it the grading system? For example, my older DD's AP Calc exams are 100, 70, 40, or 0. One mistake in an early line item and it's a 70 at best. No retakes, not half points back, no extra credit. Very, very sad if you forget +C or whatever that thing is. Did you go to tutoring? Did you do any retakes allowed? Did you join a study group? Reach out to any other teachers? Use any online study aids? Is there something in hardcopy that shows evidence of your taking a proactive step to improve or save yourself from Ds or an F? THIS is what USAFA Cadets do - they go to EI (Extra instruction), seek out classmates for tutoring, and tutor others. I think there is also an academic resource center, but not sure what they do (look at the website and core curriculum manual; I think it's referenced there).
You still have to time to improve, not just the grades, but your PROCESS. Pivot your mindset to a can-do, can-multitask attitude. Obviously through Eagle Scout/CAP you have work ethic and capacity - now just apply that to academics! Your competition will be doing this.