4.6 is a 4.6.
I am not 100% familiar with the mountaineer. But I used to race a 96 GT using excessive nitrous and blowing up motor after motor. Besides other GT's,.. I have used engines from Crown vics, Mercurys, F150 etc. Just swapped intakes and cams and that was pretty much it.
If memory serves correct,.. the 2008 Explorer and Mountaineers were rated something like 290hp. More than the 260 of a stock GT. So,.. may consider keeping the cams in place and see how that works. Depending on the mileage of the Mountaineer,.. I would also replace the timing chains, chain guides and tensioners just for peace of mind.