-I read the above thread. Incase you didn't know already, some IR ports on the back of equipment is designed to take a raw IR signal. Others are designed for a protocol specific to the manufacturer (not necessarily the same as the IR signals they use). Xantech has an interface device for the companies that use a special protocol. In my case, my Yamaha gear will take a direct IR signal. Anything else that I have I will put an emitter inside the case as you mentioned.
-Regarding taping of the IR windows: the problem is that a lot of gear hides the IR window inside the main display window. It would be nearly impossible to completely cover it without covering the actual display.
-As for blocking the IR pickup when the doors are open: the doors will open, and then slide back into the sides of the cabinet--this doesn't give me any way to hide the IR pickup (but it makes for a nice cabinet).
The cabinet is currently under construction. I'll update when I get everything setup. I'm surprised I haven't heard from someone doing this already--IR repeater systems inside a cabinet must be fairly common.