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Fossil found on the San Francisco CA coast. Fossil has snail shells but I was wondering what the smaller dark thing is.

Hey guys, Now that the weather has warmed up a bit Ive been back doing some yard work... and that means I get to bother you all with some more questions about what I've found !! So while doing some digging to run some irrigation lines, Ive been finding a lot of what appears to be clam and/or mussel shells?? I have naively posted in the past about what I thought might be possible coprolites (basically I saw a photo or two on google and connected them). But now after some time and some further research, I think some of the rocks that I posted before were actually large clams or mussels as well. The weird thing about some of these rocks though is that they seem to have retained some color. For example it appears that the body coming out of the shell of the first rock I'll post still has its colors? Like it was preserved somehow before turning into a rock? Everything tells me this is impossible... However if they are just conglomerates like others have said in the past, why would the "body" part of this rock be uniquely colored from the rest of the "shell". Is it just coincidence that this conglomerate rock has the clearly defined shape of a shell, and separate colors and composition for its shell and body? The other rocks I've found that are similar to this one all look kinda the same in that they have layers, almost like they were "folded" or "melted" on to eaechother for lack of a better word. Are there actually ways that animals could be preserved if the conditions were right? I live on mud pretty much, or thick silty mud. Could some combination of salt water, heat, some random chemical reactions, and since they are clams they could easily be packed under the mud, create an environment where it would dry, sort of like jerky lol? If this sounds crazy just let me know lol. Any comments or insight is appreciated! Ill post some others that I think could be fossils as well, the traditional kind. Previously I was told that I wouldn't find any fossils because of my location but currently I'm digging into what seems like a bed of some sort of mollusk. Also theres random sections and chunks of what looks like concrete but its not, its like hardened sandstone /limestone that I have found some interesting rocks in as well. Thanks for your time!

What is this late Miocene petrified wood found east of San Francisco, California in a watershed with Orinda, Moraga, Siesta and possibly Mulholand Formations. It is about 1.5 inches across in the photo with my fingers for scale. The other photo is taken thru microscope lens.