Assuming you are coming this month or next (Nov./Dec.) to get your MR in by the end of the year, note that the sun sets about 5:00 PM at present.

The schedule sounds packed, but may be doable. I recommend the F historic streetcar to visit the sea lions. It runs along Market St toward the Ferry Bldg, then northward (left) along the Embarcadero to Fisherman's Wharf. This year (2019) is the thirtieth anniversary of both the Loma Prieta earthquake and the subsequent arrival of the sea lions at Pier 39.

Although San Francisco is small (only about 7 miles by 7 miles), getting around takes longer than you think it will. This is due to hills, traffic, interesting sights to look at along your way, and yes, slow-moving public transit.