Pursuing a Masters, trying to figure out the potential effects of my undergraduate transcript on PhD admissions
You're right to be concerned. Some places will be scared off—or more accurately, won't even see your application—because of your undergraduate record. But some won't. Some will see your strong record in computer science, in graduate classes, and in research, at the expense of other classes as a sign of passion/focus/geekery (which is a strong advantage in research) combined with immaturity (which most people grow out of).

PhD admission is a random process, a numbers game.  You have a high-variance record, so to be reasonably confident of admission, you should apply to a wider spectrum of places than someone with a more consistent record with the same average.

I strongly recommend discussing your concerns directly with your letter writers.  They have to make the case that the admissions committee should ignore the black marks in your record and focus on your considerable strengths—good performance in graduate classes, excellence in your chosen field, strong research ability, and so on.  (You can't really make that case yourself.) Your references may also be willing to contact colleagues directly, to convince them to pull strings on your behalf.

Also: PUBLISH!

Best of luck!