The mzc66 is a tough old bit of kit and has certainly stood the test of time very well. I would consider using a dedicated control system (such as Control4) to integrate with it as this will help with controlling other devices such as an hdmi matrix and can also better integrate with your other av kit (so you don't need to keep swapping remotes etc)
I would personally avoid running long HDMI cables as they can easily be damaged and prone to potential issues further down the line. I would run 4 sets of quality cat6 to each tv point and you should have most bases covered.
Hope this is of help