Nope. Your GPAs are not competetive for the UCs, not for any MD schools. You're fine for any DO programs. High GPAs do not rescue low MCATs and vice-versa for MD schools.
1) If I end up getting my practice test score (36+), do I have a chance at any of the UC's? I can't tell if I've sufficiently made up for my low-GPA or not.
No, because you're fine for any DO program. However, if you're solely commited to getting an MD, then yes, a SMP is the way to go.
2) I was recently accepted to Rosalind Franklin's University's Masters (SMP) program with near-guaranteed admission to the Chicago Medical School if I bust my balls next year. Do you think I need the SMP?
TCOM is probably the best school for research among the COMs outside of CA. NYCOM does soem good osteopathic clinical research, as does KC-COM
3) If I'm leaving California and paying $50k+, I'd like to go somewhere ranked with decent research opportunities. Any schools come to mind? It seems like most public universities with big research budgets don't like OOS students.