I found here a book written by the Maharshal citing where pasukim are found in the Yerushalmi. In the end of this book, he cites a number of differences in halacha between the Bavli and the Yerushalmi. Is this complete? And if not, where can I find a complete list?
It is not necessarily complete; the matter is more complicated than it may seem because neither Talmud is always so clear as to how it views the final halakha, and complicated further by the fact that we don't have such a reliable text of the Yerushalmi in many instances. Most commentaries 'on the daf' of the Yerushalmi tend to minimize the differences between them (meaning, explain the Yerushalmi according to the Bavli) but their readings often seem forced.
The best book that's closest to a complete list (because he mentions everywhere that there might be a disagreement) is Amrei Bemaarava, by Achikam Keshset. The book is available online (I assume legally), at http://daf-yomi.com/BookFiles.aspx?type=1&id=36&page=17&male=0