So I installed the Kanji stroke order font (downloaded it from http://sites.google.com/site/nihilistorguk/ , then right clicked on the font and chose install). However, when I select it as the font for my answers, the font for the Heisig Kanji doesn't change; everything else uses the stroke order font, though. When I copy and paste the kanji from anki into notepad and choose the stroke order font in notepad, it displays correctly, though. Did anyone else get the stroke order font successfully working with the Heisig Deck in Anki?

Yes it is working. Is Kanji set up to have a unique font from the answer? If so, make that font the SO font.

EDIT: instructions
Settings > Font settings > click on second tab, "Fields", then click on the item Kanji below and add a custom font below.

Ah I see, I was completely missing the fields tab. Thanks!