I am not sure why you don’t seem to hear what we’re saying.
We’re not discouraging you to put you down. We’re trying to get you to see the writing on the wall.
No, the cc classes are not ECs. No, side programming work won’t make up for a B in math (assuming you can retake the physics and get a A and the former class is wiped out.) Plus, you’re a junior now. Taking the replacement course as a senior, you won’t have the new grade to show and the prior physics may very well still sit on your transcript.
No, when they have tens of thousands of apps, they don’t have to say, “Oh, dear, it was one bad semester.” Lots of kids have challenging teachers.
No, they don’t want extra LoRs from reearch mentors. Yes, they will want to see a CS kid with a great physics LoR (or second choice, a math LoR.) (UC may not even read LoRs.)
No, your issue is not just gpa and one poor semester. Your thinking is off. How do you expect to pull together a successful app when it hinges on excuses, them accepting your first semester of jr year is a fluke…while you don’t know how to self match? What do you rally think they will see in your full app that will make them say, “Yeah!” over others?