Don we have had our Chack Chack on the delta since March. You would like Korths on Brannen Island as a base, or if you want a nearby town Delta Marina in Rio Vista is very nice and you can walk right into town. Nice places to visit in no particular order are - on the Mokelume - Giusti's a classic delta restaurant with dockage overnight for ten dollars including electricity, then on up the Mokelumne to the Meadows for an overnight anchorage, Wimpys on the the South Mokelumne is quite and they let us stay on there dock for free. Tower Park is a little loud and busier but another fun stop. Up the Sacramento go to the Old Town city docks in Sacramento then up to the American River to Potluck Beach. On your way back to Rio Vista take Steamboat Slough.
Other popular anchorages are Potato Slough and Mandeville Cut
We have found the least expensive fuel at Pittsburgh and for you that might be a good place to leave your boat as you can take Bart back to the city. The marina there is excellent and there is a nice brew pub, and a few nice restaurants within walking distance
Everybody tells us not to go to Stockton so we just have been there but I know they invested heavily in there marina
Then you have another 1000 miles of waterway at your disposal just to explore
Cheers
Eric
PS if you do go to Rio Vista walk into town and make a stop at Fosters Big Horn not environmentally correct but worth the stop