Well, the first thing mobipocket creator does in creating the prc is reading the pdf out to a html file. You will find the html file in the same folder as the prc. Then you open the html file with sigil http://code.google.com/p/sigil
(it takes a while to load the html) and go to 'Edit/Replace' - a dialogbox will pop up with a 'Find X - Replace with Y' possibility. Sigil will save the html file as an epub, that means you'll still have to convert it to mobi but it's the best tool to make your ebooks shine.