Okay, I'm just going to quick-reply this: if you have a mobi file, you can put it into Calibre (yeah, yeah, I know, I am not crazy about that either) and try to convert it to something else (anything) and set the debug option, which should deposit one big long honking html file in your Calibre Debug folder. It ain't pretty, and I wouldn't suggest it to most folks, but if you GREP, you could fix that pretty quick. Which would give you ONE file to slam into Sigil, methinks. Try that, and see if it works. You should be able to regex all the flattened css back into "real" css in your ss's.
Also, gotta tell ya--have never seen a Calibre ePUB ePUBcheck, ever. I like Kovid; I like his work, and Calibre is, in its own way, Mighty; but they simply don't pass, long, short or otherwise.
HTH,
Hitch
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