sf2sd: Our family is actually looking at doing the reverse of your move. From SD to SF. We are also transplanted East Coasters. We have scouted the Bay Area a bit and like Mill Valley and some east bay areas around Walnut Creek. Any insights, based on your same criteria? Our budget’s half of yours, so that would be a factor. Same deal though–kids need good schools, nice community feel, easy commuting options are high on the list. Want to live there a year or so, scout out areas, then look into buying.
As for San Diego, Encinitas is quite nice–we have friends with kids and they have had a great experience there. Are you averse to moving further south? You might like some of the outlying areas of La Jolla (in between downtown La Jolla proper and UTC, the latter being comprised mainly of off-campus housing for UCSD). I think the area I am thinking of is called La Jolla Farms (lots of professors live there) as well as Mt Soledad. Lastly, my favorite, but far south, is Coronado. VERY family friendly, good schools (public), has a great small town, community feel (you will start to know and recognize people within the first 3 months you live there). Your buying price range will put you into a small house here, but most houses here are 3-4 BR beach bungalows, so beware if you are looking for something bigger.
You could also look into Poway (east of I-15) as they have a great school system and the newer area Carmel Heights (?–the exact name is escaping me), etc. Others here can probably chime in on these. The area is newly developed so lots of tract housing, but I hear the schools are good.