learning enough regex to get by is the key. there is sufficient in the forums & online or in a simple book like "sam's teach yourself in 10 mins"
I think the issues break down into:
1. formatting - mostly line break issues, but also there's malfunctioning special characters like accents & dashes.
2 chapter detection & headings. - once you get to understand what e-reader software looks for & how calibre handles heuristics - they are not so bad.
3. typos / scan errors
2of 3 can be fixed well with calibre & sigl
3 needs the most manual input, but if a word is mis-scanned once it's likely to be consistently mis-scanned through out, so I use find / replace to look for other instances e.g. find all I'11, replace with I'll.
there is a spell check free tool ( microspell ) that will work with Sigil and/or will scan your txt files, but I've found it too troublesome for regular use.. it has to be taught all the proper nouns anyway then it develops a tendency to accept some scan errors as uncommon words & has to be retrained... if you have the patience, it does have lots of options & can learn as it goes....
http://www.microspell.com/ seems to work OK in windows 7.
stripping header & footer ( & page numbers ) is only an issue with .pdf sources, which are best avoided anyway.
when it comes to fine tuning book appearance, then a little understanding of HTML styles & the stylesheet.css file ( editable in sigil) goes a long way. I keep goggling & asking whenever I bump into something that I don't fully understand.