This is WAY too detailed to be looking for generic advice over the internet. For one thing, without knowing what state you lifve in, it is difficult to know what the applicable law would be, let alone trying to apply it. You need to make an appointment with an attorney immediately to discuss this. I think you definitely have some issues here, but they are not easily answered in this sort of forum.
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The previous answers are on point. I would also suggest doing a search of blogs and a general Goggle search using S-scorp and LLC as variables - there's a whole bunch of stuff written on this which should be useful to you in making the decision. Attached is a posting from my blog which -- though focused on Ohio law rather than CA -- may help answer some questions. A couple of things to check - I know in some states (and I think CA may be one of them) there is a frahchise tax for LLCs and...