not a mustang question but indead a 4.6 question

I would think that the reason it makes power lower is due to the trans and rear gearing. The tune would probably be different too.

I swapped a 4.6 from an 04 grand marquis into a 00 stang w/out too many issues. All the PI 4.6's are pretty much the same...only differences are small things like PCV location, oil pan depth...maybe injector size.

Here is what you do. Look at both motors and see how many valve cover bolts each has. This will determine if they are romeo or windsor. Romeo has 11 and windsor has like 13 I believe. If both are the same then you should be ok. Is the stang motor an auto or stick? You may have to change over to a flex plate or flywheel depending on application your truck has. I believe the injectors are the same though. It will have more power of course due to the PI engine. You shouldn't have a problem at all. Might need to change over the oil pans too. The main thing is to make sure they are either both romeo or both windsor. Because there are differences between the two of them. Such as crank bolt holes and front covers etc.... Good luck on the swap. If you have access to a lift you might want to lift the cab to do this engine. Its the easiest way and really saves on the back. Have fun.