1) SHORT CODES
I am using a really cool Quote plugin called Flexi quote rotator I have an option to use the short code or insert a PHP snippet in template is there a way to accomplish with out hacking an actual page? If not, please let me know the best place to add the code.

2) SIDEBAR NAVIGATION
Are there any options to have a dropdown on the sidebar navigation? Currently the sidebar is 3 levels and I don't want all of them to show. I am also trying to avoid adding the page id's to the exclude list.

How can I use a favicon on the sidebar navigation menu? Here's a link the site
http://www.earacupunctureresources.com to so you can get an idea.

One solution to your first question might be to use the exec-php plugin as well and then place the php code in a text widget - that way it is widgetized so you can move it around and it should still work as described/advertised.