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Not sure whether it was a typo, but you don't want line un-wrap set to '1', you want it set to '.1', note the decimal point. And you only need it set to that for books where a small percentage of lines are unwrapped, the defaults should be good on a 'typical' book with hard breaks (e.g. pdf, many text files, some OCR sources). Setting it that low on a book where every line has hard breaks will cause poetry, etc to be un-wrapped.
It's possible that's the cause of your remaining splits.
If the original source was a pdf, it's possible that the pattern used to remove the headers and footers didn't delete the surrounding tags associated with those headers and footers - that leftover garbage can trip up the later work Calibre does to try and fix the line breaks, etc. If you're not the one doing the intial conversion there's not much you can do to fix it at this point...
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