I have had the same issue on a few Stangs. The way to break the seal of a stock shifter is fairly easy. Take a 3 to 4 foot 2X4 and place it at the base of the shifter. Then, with one quick blow (I used a rubber mallet) off she'll come.
Don't forget to scrape off the old gasket sealant, and reseal it with a high temperature gasket sealant.