Your GPA is the only thing really holding you back. But since it’s mainly your freshman transcript that’s mucking it up, you shouldn’t worry too much about it.
If you applied engineering to some of these schools then your chances may go down slightly, if not more. That being said, you have a strong application regardless. Your breadth of extracurricular activity is matched with depth. This is always a good thing. You’re applying to a lot of UCs as an OOS applicant so that won’t be too much in your favor, but as I’ve said already, you’re a strong applicant.
UCB: Low Reach
UCLA: Low Reach
UCSD: High Match
UCD: Match
UCSB: Match
UCI: Low Match
U. Chicago: Low Reach
Duke: Reach
Wash. U: Reach
Michigan: Low Reach
Vanderbilt: Reach
Johns Hopkins: Reach
Stanford: Reach
Cornell: Reach
Princeton: Reach
Note that your chances at these schools are good as a regular applicant. However, I had to take into consideration that you applied for engineering. I mean all of these schools have such highly coveted engineering spots and boast some of the best engineering programs in the world. Your GPA and subject tests are going to count against you because engineering is so academically aggressive in terms of test scores. You’ll be up against kids who have perfect GPAs and test scores, but your ECs should compensate for a bit of that.
Whether the adcoms will view you as a more well-rounded student or as a student lacking in the typical traits of an ideal engineering candidate is up to them.
Best of luck!