This question is so detailed I won't be able to answer half of the questions.
There are many marinas in the Delta that offer good overnight facilities. Delta Marina in Rio Vista would be a great first stop for you. Fine facility with The Point restaurant and city of Rio Vista is a short walk away. Historically, Delta Marina has some of the least expensive fuel in the Delta.
Spindrift Marina, where we berth the boat is nice for an overnight and has a great restaurant right next door, on the levee.
Everyone will tell you that their marina is the best if that's where they stay. You really can't go that wrong with nearly any of them.
Here is a good starting point:
http://www.californiadelta.org/deltamarina.htm
Piper Slough along Bethel Island is on the west side of Franks Tract. Several good places to tie up for the night there.
One of the things I like about the Delta is that it's so easy for cruisers just to anchor out for a night. We will stay overnight at a marina once and a while, though.
Here are the pump-out facilities:
(FYI: Location (nearest location) of California Delta marine sewage pump-out stations. No operating hours provided, though. The following info is from 2003 data compiled by California Coastal Commission’s Boating Clean and Green Campaign…)
Contra Costa County:
Point San Pablo Yacht Club (tenants only)) (Point Richmond)
Richmond Marina Bay Harbor (Richmond)
Holland Riverside Marina (Brentwood)
Lindquist Landing Marina (Brentwood)
Discovery Bay Yacht Harbor (Discovery Bay)
Martinez Marina (Martinez)
Lauritzen Yacht Harbor (Oakley)
Richmond Yacht Club (tenants only)(Richmond)
Bentley’s Marina and RV Park (Bethel Island)
Sugar Barge Marina (Bethel Island)
Mariner Cove Marina (Bethel Island)
Antioch Marina (Antioch)
Casa del Rio Motel and Marina (Oakley)
Caliente Yacht Club (Bethel Island)
Pittsburg Marina (Pittsburg)
Driftwood Marina (Oakley)
Harris Marina (Bethel Island)
New Anchor Marina (Bethel Island)
Sacramento County:
Brannan Island State Park (Rio Vista)
Willow Berm Marina (Isleton)
Cliffs Marina (Sacramento)
Boathouse Marina (Locke)
Riverbank Marina (Sacramento)
Oxbow Marina (Isleton)
Eddo’s Harbor (Rio Vista)
Freeport Marina (Sacramento)
Dagmar’s Landing (Walnut Grove)
Delta Bay Marina (Isleton)
Metro Marina (Sacramento)
Korth’s Pirates’ Lair Marina (Isleton)
Sacramento Marina (Sacramento)
Walnut Grove Marina (Walnut Grove)
Landing 63 (Walnut Grove)
Folsom Lake State Recreation Area (Folsom Point Ramp)
Folsom Lake State Recreation Area (Granite Bay 4 Ramps)
Lighthouse and Resort Marina (Isleton)
Folsom Lake State Recreation Area (Rattlesnake Ramp)
Rancho Marina Resort (Isleton)
Snug Harbor Marina (Ryer Island)
Dagmars Landing (Walnut Grove)
Ko-Ket Resort (Isleton)
Vieiras Resort (Isleton)
San Joaquin County:
Waterfront Yacht Harbor (Stockton)
Tiki Lagoon Resort Marina (Stockton)
H & H Marina Resort (Stockton) (tenants only)
King Island Resort (Stockton)
Village West Marina (Stockton)
Paradise Point Marina (Stockton)
Whiskey Slough Harbor (Holt)
Tower Park Marina (Lodi)
New Hope Landing (Thornton)
River Point Landing (Stockton)
Stockton Yacht Club (Stockton)
Solano County:
Benicia Marina (Benicia)
Delta Marina (Rio Vista)
Suisun City Marina (Suisun)
Vallejo Municipal Marina (Vallejo)
Glen Cove Marina (Vallejo)
Hidden Harbor (Walnut Grove)
Sonoma County:
Petaluma Marina (Petaluma)
Port Sonoma Marina (Petaluma)
Spud Point Marina (Bodega Bay)
Yolo County:
Sacramento Yacht Club (Sacramento) (tenants only)
Sherwood Harbor Marina & RV Park (W. Sacramento)