Welcome to the board Stacy!
My husband and my youngest son have EHK. David has had 2 experiences with MRSA. Fortunately for us it was the community strain and not the hospital strain. Both times the medications worked well for him. After his second infection his pediatrician strated him on a maintainance medication that we put his nose once a month for 5 days. We also add bleach to his bath and the combination has been extremely effective!
As for the scratching- we have never really had this problem with David. We keep his nails cut really short and the few times he has been scratchy we got away with an over the counter hydrocortizone cream. Unfortunatly it does not sound like that would work for Breyden.
Have you tried benedryl or Zyrtec?
Happy New Year!