This is how I deal with text PDFs:
1 - Crop headers and footers with
BRISS.
2 - Import and convert with
MOBIPOCKET CREATOR professional edition.
3 - Import the HTML output form MOBIPOCKET CREATOR with Sigil.
4 - Correct and apply the desired formatting with Sigil. Depending on the PDF, this may take from some hours to several days.
Good luck
PS: Both BRISS and MOBIPOCKET CREATOR are free.