I've read the 2011 DS14MK4 guide and verified the loop speeds are all set consistently and IDs are all unique. (note: trays IDs are 1-4 from bottom to top)
Can I simply:
1 - remove the top two pairs of fiber and transceivers (these go to head 1 (partner))
Not sure what you are saying here. Both pairs of fiber from the same shelf shouldn't be going to the same head in an MPHA config.
Properly done, MPHA has head 1 connected to shelf 1 ESH A and head 2 connected to shelf 1 ESH B. Then the last shelf in the loop has ESH A go to head 2 and ESH B go to head 1. The way to think of it is that the primary path is 'forward' through the one loop and the secondary path is 'backward' through the other loop. Traffic on each loop is in both directions, but thinking forward and backward through the loop helps me visualize it better.
If MHPA is properly configured, you can disconnect the fiber at the end of the loop, connect the new shelves, and then reconnect the end of the loop to the new last shelf in the loop.
I'd recommend running ConfigAdvisor (in the toolchest on support.netapp.com) to verify your configuration both before and after adding the shelves. It verifies MPHA configurations, among other things.
John