you are quickly finding out why Pros dont use harmony. you will also soon find out why you should replace your apple gear with a real router.
you have saved the money on doing everything yourself, why dont you bring in a pro to install something like Control4? EA1 with SR260 remote is $599 plus whatever your local CI charges for programming/installation. a setup like yours (assuming its half way correct) would take no more then 2 hours to install and setup/program. aside from a great platform you also get control of your system from your mobile device...its nice when the couch eats your remote or its in the other room! besides, its stupid easy to expand!
The Bitterness of Poor Quality is Remembered Long after the Sweetness of Price is Forgotten! - Benjamin Franklin