I love the idea. But I'm sure there would be fitment, wire harness and computer issues, unless your into modifications and hacking Honda technology.
What's wrong with the engine you have? The engine blocks are very bullet proof, unless it was abused some how.
Biggest differences between the two are the Heads if both are J35's. So if you simply swapped blocks, the computer likely wouldn't be the wiser. Messing with the head means messing with the tune, and you can't simply drop the computer from your Accord into the Pilot. Unfortunately with immobilizer systems and everything else, easy ECU swaps are a thing of the past. Like my old Accord and Preludes with the same motor (F22A1), could get a 10hp or so increase in power simply by swapping the ECU from the Prelude into the Accord.