I can't attest to how to estimate this type of job. But there isn't anything to prevent you from getting 3 estimates. Get as much info as you can. Then, call up COntractor A and ask why he's more (or less) than Contractors B & C, and so on. By the time you're through talking to 3 contractors, you're a much more educated consumer. It's OK to be 'naive' with the first contractor or 2. But by the time you're finished w/the third one, you'll be surprised at how much you know!
If you go for a re-wiring job, consider asking for a separate estimate to run phone and cable wire to the rooms too. (NOT necessarily ALL the rooms - maybe just a few, your call.) These days, with cable-modems and satellite TV, almost EVERY room needs some sort of 'modern wiring' for computers or TVs! Speaker wire wouldn't be such a bad idea too (for a room or 2.)
My best to ya and hope this helps.
PS: If 200 amp is 'normal' for the Bay area, and you don't have it, find out what is 'normal' and get the upgrade (if you don't have the 'normal feed' into the house.) In my area, 200 amp service is 'normal' ... That will cost a few $$$ to have done.