I went to a 4.6 about a year ago. Found the following, swapped ecu's back and forth and found no difference. You need to watch your source block for the fixing for the crank position sensor. A genuine 4.6 (say from a P38) will have a different alloy plate fixed into the back of the block. It's not a hard swap from you original block but you should do it before you get it all assembled (sound like voice of experience?). If you get a hatted 4.0 then it should be ok.
Sourcing the bits to upgrade could be harder than you think. Make sure you fit studs to the heads and main caps. Ring around the wreckers, I picked up a 10,000k rebuilt 4.6 for $2200-. Spent more than half of that in the previous 6 months chasing blown head gaskets.
If the MAF is original plan to replace anyway. You'll know about it when it goes.


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