Okay, after spending a while going through all the settings, I found the combo that makes the print look nice, validates well, and avoids the non-standard ” tags.
Turn the following on (all others off)
break-before-br
clean
doctype=auto
drop-empty-paras
drop-font-tags
drop-prorietary-attributes
enclose-block-text
enclose-text
fix-bad-comments
fix-uri
indent-cdata
join-classes
join-styles
logical-emphasis
lower-literals
ncr
numeric-entities
quote-nbsp
repeated-attributes: keep-last
word-2000
indent=auto
indent-spaces=2
markup
tab-size=2
wrap=75
wrap-asp
wrap-jste
wrap-php
wrap-sections
char-encoding=ascii
output-bom=auto
fix-backslash
keep-time
write-back
Obviously, not all of these have anything to do with the original problem of entites changing from " to " etc, but for those who want nicely-indented, correct html, these settings will do it for you.
Cheers