Hi Paul,
We've recently completed a legacy storage to FAS3140 (rebrand) Exchange migration. We had consultant help every step of the way, and the correct procedure in their experiece is to remove ALL vestiges of MPIO support from your legacy vendor, but do not install the NetApp DSM for MPIO until your migration is completed.
We ran for two weeks with single-intiator-single-target zoning from both arrays while we migrated. We installed SnapDrive and SnapManager for Exchange, but not MPIO, and used SME to perform the migratition.
I am at a loss for the proper NOW and KB articles, but I believe that multiple MPIO installations are not supported by any of the vendors we were dealing with. It was just a risk we need to accomplish the move.
Once Netapp DSM for MPIO was installed, we brought the cluster completely down, rezoned using single-initiator-zoning to all target ports, and booted without any trouble from the MS cluster. It just sort of worked and made us happy.
I hope this helps. I will try to find the supporting documentation.