maxfields2000, I give you credit for venturing into the unknown and learning as you go.
About the prefs syntax change, this is one of the biggest changes from 1.9 and 1.10 as far as the template files are concerned because it's global and affects a lot of files. While there is an admin switch to allow use of the old syntax, the forward-looking approach is to use the 1.10 syntax. Replacing $feature with $prefs.feature in templates/styles/(themename) takes care of most of these. I've done that for a few themes already now.
At http://zukakakina.com/110_theme_upgrade_issues I made a table of some upgrade issues I had run across, which may be helpful. (This was on my local (laptop) test site but I put it at Zukakakina in case anyone can use the info.) This isn't complete by any means but has some of the most apparent things.