I'd suggest doing a 3L if you are going to go to all the trouble of pulling the transmission out. There is almost no difference in time pulling the transmission then there is pulling the entire motor and transmission out. If you can wait save yourself a lot of time and money by doing it all at once. If your not going to do a 3L then forget I said anything. At the very least do headers for the car. One of the best mods for our cars.
1999 3.0L Cougar: 220fwhp and 200tq
2003 VW Passat W8 with 4 Motion AWD
http://www.cardomain.com/ride/300644
PM for intrest in 3L SVT Contours, 3L swaps into your current car, Prepped 3L engines, or anything 3L related.