Need Suggestions

That sounds like a cool project. Although I have never done that myself, and it doesn't seem really common, I'm pretty sure I have seen somewhere a thread or two where somebody did something similar.

About the powerhead cords, running them up through a conduit that comes through a bulkhead is an option, depending on your tank layout. Most commonly it's done for tanks with a center island overflow. You just want to make sure your bulkhead and conduit (PVC) are of large enough diameter to accommodate fishing the plug through. Sometimes you may have to trim off the rubber edges of the plug to make it fit, or even cut and splice the cord (just make the splice OUTSIDE the tank before the cord enters the conduit, for safety). You may have to cut and splice cords anyway to get pumps out to service them if there are several cords running through the conduit.

Regarding powerhead positioning, there are plenty of opinions to go around. I personally think it is a good idea to put at least some kind of pump down low depending on the tank size. I like to put them kind of behind the rock stack in the cavernous areas out of sight, just so they can help circulate water through areas that may not get much otherwise. As long as your main pump is providing descent surface agitation for gas exchange I wouldn't worry about pointing the powerheads up. Just get that water flowing out from the potentially stagnant areas into a stronger current, and it will get circulated. Of course depending on your corals, you don't want to have chaotic currents in every inch of the tank. Some corals prefer calmer areas.

With silicone, you could buy tubes of "aquarium sealant" from the LFS, but probably the most cost effective way to go (and it's safe) is to buy GE Silicone I from Home Depot or some place. I just buy the clear flavor, but make sure it says "Silicone I" not "II" because the II has a mildew resistant ingredient in it that can potentially harm sensitive microorganisms. So the Window grade silicone will work, not the bathroom grade stuff.

I have bent a lot of plastic, and the best way I know of is to use a torch or heat gun. I'm assuming the eggcrate will act as a lath to help adhere the rocks and mortar, so it doesn't need to be really pretty since you'll never see it.

Good luck. Post pics!