I got it working with this. I had to enable the line spacing and custom font patches and disabled the epub custom header and footer margins.
Code:
# Example for AuraHD/H2O:
replace_string = D54355, `min-height: 70px;`, `min-height: 36px;`
replace_string = D54368, `max-height: 70px;`, `max-height: 36px;`
replace_string = D54385, `footerMargin: 40;`, `footerMargin: 20;`
replace_string = D5439F, `font-size: 16px;`, `font-size: 26px;`
replace_string = D543B1, `padding-bottom: 0px;`, `padding-bottom:10px;`
replace_string = D543C7, `margin-top: 0px;`, `margin-top:-8px;`
#
# Uncomment one of the following if you wish the footer to use a fixed font.
# (And enable one of the Custom header style patches below using the same font.)
#
#replace_string = D543D9, `/*font-family:none;*/`, `font-family: Amasis;`
#replace_string = D543D9, `/*font-family:none;*/`, `font-family: Avenir;`
replace_string = D543D9, `/*font-family:none;*/`, `font-family: Georgia;`
#
There is still extra space with the book I stripped all css out of but it's not really a big deal.
edit: I reconverted that book but didn't strip any css and just added 'body {orphans: 1; widows: 1}' and it works properly now. Thanks everyone for all the help!
edit#2: Updated the code to include the font I'm using for the footer.