I would recommend using a better HDMI extender - those wall plate, "unpowered" models have not been exactly bullet-proof.
In addition, if you're expecting to use any of the less-expensive HDMI extenders that consume 2 category cables, you should run a third category cable to each TV location - so that you have Ethernet capability (or something else) in addition to the HDMI-over-category path.
-I am running a Cat6 drop to every room in addition to what is already there for keypads and tv's. I will likely locate these in areas that are likely to be covered by furniture like nightstands and desks. This will also be my fall back for telephone jacks if I ever decide to put them in. For now, I have no desire to put a bunch of additional jacks for telephones when I haven't had a traditional landline in years.
My rule of thumb for bedrooms is to have access to a cat6 jack from any usable wall space in the room without crossing a door frame. Which for most bedrooms means two locations per room.
-I will use iRule to control everything via ios devices in addition to the keypads. I am not sure if I will need the HTD ios setup or not.
If you're going down the iRule path you'll really want the HTDnet adapter, even if you don't use their app...
I will have them plywood the walls and run two dedicated circuits for power to it. I will run a low voltage fan up out of the top of the closet and the doors will be louvered.
Where are you exhausting the air to from the closet - you don't want to dump that into the attic or outside. The HVAC return is a good choice.
-I have two colors of Cat6 to help with distinguishing them, especially where they are run together. Any wire labeling systems or devices work really well?
Rhino label maker.