Last year I had an Energizer kit put on my YJ by the guys over at MPD. Now, first and foremost, I totally trust Jack's work. It's just that ever since then, I've been going through bottom ends. I'm pretty sure it's not the pump's fault but I'm getting ready to put another 455 (oil mods done, details in another thread) together and I'm a bit paranoid. :220v:
In answer to your question, it is possible for incorrect engine installation to put the pump in a situation where it could damage the thrust bearing on the crankshaft of the engine. Sometimes the impeller will want to walk forward in the housing. If you have your driveline bottomed out on the input shaft of the pump and the impeller/shaft walks forward just a little bit it could put enough pressure on the thrust bearing which would tend to put some debris into the pan.
What is probably more likely is that you are now spinning your 455 at higher RPMs and maybe for longer periods of time than before the energizer kit? Or possibly that you had a rod or main go south once (pretty common on 455s) and it did some damage to a part that hasn't been properly repaired. Now that part is continuing to eat stuff up. I had a problem with a concentricity with one of my main journals in my bbc caused a couple rebuilds before the problem was properly diagnosed. You might want to take a bore gauge to your mains and rods to see if there is something going on in the motor.
Just the same, I'd also take the boat down to MPD after you get the new mill in and have him check your driveline out to make sure you're not in a bind or something. A lot of times shops do work on one specific part of a boat and never see the rest of the components or how they are bolted together. Then when something goes blam, they get blamed. It could be something simple where if MPD sees the entire installation, it will stick out like a sore thumb.
Good luck with it, and rest assured, you'r in the best hands in the business as far as the pump is concerned.
Chris