difference between 4.6 and 5.4
 

I know they have the same bore, are the cylinders taller on the 5.4 or do they share the same cylinders?

Granted I'm no expert, but assuming the bore is the same that means the stroke would have to be longer meaning that the 5.4 would have longer connecting rods and a larger crank.

Krunker, don't you mean shorter connecting rods and a longer stroke on the crank?

I realize it would need a longer stroke but do they share the same cylinders or are the 5.4's taller?

Ya, that sounds more like it, although I think the 5.4 is also a little taller and wider. I have the manual for 1997 and newer F-150's, I'll consult it and report back. Also, when you ask if they share the same cylinders, do you actually mean pistons or the actual liners in the block?

The 5.4L block is taller to accomodate the longer stroke. They have the same bore.
The stroke on the 5.4L is 4.14". The block is taller and wider so the intakes will not interchange. The bolt on accesories in the front will interchange. The heads are the same as well as the camshafts.
If you are looking to upgrade from a 4.6L to a 5.4L, check out Ford's new 5.0L Modular engine with a redesigned block for a larger bore with 4.6L stroke.
Jimmy

Difference between 5.4 and 4.9 motor
 

I have a 04 150 5.4 FX4 and have the option to buy a 04 4 wheel drive with the smaller motor but bad transmission.. my question: will the auto transmission in my truck (75) work with the smaller motor?