Calculate your UC GPA’s here: GPA Calculator for the University of California – RogerHub
If you’re applying to UCSB for CS, consider also applying to the College of Creative Studies computing major, which has its own additional application: Computing | UCSB College of Creative Studies
When you apply to SLO, make 100% sure to include all high-school-credit classes you took in middle school, in the correct spot on the application. Every year, we see otherwise-qualified applicants slip below the acceptance threshold because they forgot this.
Talk to your college counselor at school before the end of this year, and discuss the issue with the semester when you were sick. It is better for this to be explained in the counselor recommendation than for you to mention it. Use your application for the positive stuff, not for extenuating circumstances, which will play better coming from the counselor.
If you’re interested in MIT and Mudd, are you also interested in Caltech?
If you like Mudd and the Claremonts, you might consider applying to Pomona as well. (I would have recommended Scripps as well, in the past, but it seems that the ability to choose an off-campus major in CS through Mudd or Pomona is no longer assured.)
If you like Columbia, you could apply to Barnard as well.
UMich could be worth a look. (They have CS both in L&S and in Engineering)
Are you considering applying to USC, to see if you land one of the big NMF scholarships? If you like the Boston schools, Northeastern has strong CS and a pretty generous NMF award (it used to be a guaranteed 30K - not sure if that’s changing). There are also good CS schools that you could attend for free with NMF - UT Dallas, for example, or Arizona as TSBN suggested - these could make good safeties. (If it came down to it, a free ride might beat paying 35K/year for Merced, for example.) There are good safeties with WUE reciprocity that would also give you merit - Utah, for example, or UNR.
You’re a strong applicant and you should have good options - just make sure you apply to a range of schools and that you have safeties you could be happy with. Is there anywhere that you want to apply Early Decision, or would you prefer your most-desired UC(s) and/or SLO over the schools that have ED?