I'm relatively fresh out of school (just over a year full-time at my current job) so I don't know that it'd be as easy to just switch now without looking like I hop job to job.
Moving jobs after a year is very common in tech. If you have any co-workers who left, asking them for referral (if they like the new gig) is a great way to go about it. Lots of companies pay referral bonuses so your old co-worker will be happy about it too. I'm on my third job after graduating and have more than doubled my income in 3.5 years.
A year in is a perfect time to hop IMHO.
maybe you could swing 3 remote days a week at some point?
Possibly; my manager basically already does that, but then he's a manager so he has the rank to do it.
You should use the long commute as leverage, i.e. you need to either work one more day a week from home or start looking for something closer to SJ. You won't come off as looking disloyal to the company because everyone understands how brutal that commute is.