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The Columbus Ave. loop seems extraneous to me when a simple bore to Kirkland Yard under Bay would do. That's all fill and mud.

I cannot imagine upscale Union St. wanting a station with the homeless and junkie baggage. So Lombard St. remains. It would be the height of retrograde stupidity to do an underground at grade wye north of Washington Square so you would have to grade separate similar to Market and Duboce. Gotta be very spendy if you can find enough room. The grade is downhill and you are already pretty far north.

Muni would be better off planning their future Marina express rail line tapping into a Geary line via a tunnel under Pacific Hts. from Lombard and Fillmore.