So far, the only issue that you mentioned that seems to be related to SpamSieve 3 (rather than a Mail issue) is this one. Please go there and try the fix that I suggested.
There was a month of testing as a free public beta, with over a thousand testers, and no one reported any of the issues that you have. It seems like there may be something wrong with Mail’s files on your Mac.
In contrast, @jennifer seems to be running into two known issues that were already in the FAQ, neither of which is a bug in SpamSieve.