Some pictures might help, but it sounds like you've got a decent handle on it so far. The one thing to consider when wiring (in any application), is always pull more through than you need, and if possible (or practical) run spares. Last thing you want to discover after going through all the trouble is a bad cable that's now buried behind the drywall, etc. Not likely, but it does happen - an errant drywall screw can wreak havoc on an HDMI cable.
Some other considerations - if you suspect that you might ever use any of the TV's other inputs (for example, VGA connection for a PC), DVI, etc., be sure to run those cables too, and leave them hanging at your rack if necessary to make future expansion easier.
Also, don't forget your basic electrical considerations. Make sure you have adequate power in the A/V closet for your gear, as well as having the electrician put in a receptacle at the TV location. If possible, have them place the receptacle in a recessed enclosure within your wall behind the TV, so that it will not interfere with the TV when you go to mount it. That way you can put it right behind the TV (out of sight completely) and never see it. Don't forget your sub either.
Speaking of which - I might avoid putting your sub in any kind of cabinet.
Lastly, if you're using an RF repeater system - might want to run one to the TV with that HDMI.
