re: What major US city (like top 50) would fare best?

While very few areas will be able to handle this type of rain and go unscathed, San Francisco itself would handle it better than most would expect. It's the west side of the surrounding counties of Sonoma, Marin, Santa Clara (San Jose last year) and San Mateo that would be under water. They are very prone to flooding and mudslides in years with above average rainfall (like last year). Petaluma (where I've lived for the past 30 years)-has some big time flooding when we get a storm that dumps 6-8 inches over the course of 2-3 days. 45-50 inches in 72 hours=toast.