i could be wrong but arent the 99-02 computers different than 03+ ??? i cant tell for sure from your post but it seems like all you did was swap the motor only.... if you changed the harness and pcm then nevermind.

but i also had the same problem when i first tried starting mine. it was a missing ground. yes one single ground wire prevented spark. the one apararantly a lot of people miss. its on the driver side of the block down low. check ALL your grounds as they are VERY important.

as soon as i connected it, she fired right up. good luck