Hi Ron.
Congrats on your prize! I have a biocube 14, and I've done well with very basic mods.
First off, I've replaced the stock pump with a maxijet 900 (for me the MJ 1200 cause a heat issue, but may be fine for a BC 29). I've removed the BioBalls. I have a Sapphire Aquatics
skimmer in the 2nd chamber (the company has gone out of business). I also have a plastic strip that i salvaged from a 10 gallon aquarium cover along the back edge of the display area to prevent my clown fish from exploring the back
sump area.
The stock lighting has been adaquate for my mushrooms, zoas, xenia, candy cane, open brain and torch coral.
I agree with Phurst's assessment of your original stacking plan.
Good luck!
HTH