just for people who may be interested i just finished the 5.4 swap in my 03 gt, ive got about 800 miles on it so far and its been no problems so far not even a check engine light, i am using the gt 5 speed transmission still (tr-3650) i had to swap to a 8 bolt flywheel, luckily i made a drive to georgia to get one from a guy and he ended up just giving it to me and i believe its a fidenza aluminum flywheel that was meant for the 99-01 gts, but it works on the 5.4 and i could still use the 11...

5.4 swap complete !!