After reading scottwells post earlier, I did some reading and found the same thing bobray posted. For some reason it didn't work, though I saw it on several websites. I did finally find what I thought was a fairly elegant solution, but if someone has something better I'm all ears.
First I run through this, which works beautifully for removing my "smart apostrophes":
$entry->set('ProgNotes', iconv('UTF-8', 'ASCII//TRANSLIT', $entry->get('ProgNotes') ) );
Then just to make sure I get rid of all the obnoxious Microsoft formatting I put in a second line to get rid of everything else the first line may not change:
$entry->set('ProgNotes', preg_replace('/[^(\x20-\x7F)]*/','', $entry->get('ProgNotes') ) );
While I'm not 100% that this is the best approach, it is the only one that worked after several attempts to solve this annoying problem.
Thanks for the feedback guys, it helped.