Well I've finally made some progress.
I took the suggestion to try different code pages. CP1252 replaced the missing apostrophe/single quotes, but prefixed them all with An "A" with a caret on top.
I then used the Calibre "tweak ePub" function to open the source files, then did a search & replace on all the unneeded characters. A bit of hassle, but I seem to have a serviceable novel.
Thank you to all who posted suggestions! I'd be lost without your help.