98 250 5.4 engin shot 04 xl 4.6

will change out the trans also
exahust going to be modified from what I read

1. since both are two valve can I use the 5.4 pcm ( the 4.6 no more ) but I can get one.

2. will it go? engine is free labor cheap me and the kids we have four trucks now down from six and we do all the maintance and fixing, so not beginers but not experts either ( by far ) also not a lot of older 5.4s here

I read a lot about going to a 5.4 from a 4.6 but found nothing going the other way.
thanks