1. I am wondering how they get the different colors/intensities in these commercial systems? You mentioned LED's only have one intensity...? (Maybe they are just using colored lenses?)
2. As I'm not thinking for lighing on a plant tank or freshwater tank... Can I build a system that is going to work with a reef?
3. What do I need to know? (Now that's a 'black & white' question in a field of 'gray'!...LOL)
Not being too electronics saavy, if your post wasn't darn so friendly, and fun... I would feel really unsure about asking for my particular stuff. But you are really a fun read (even if I don't always understand all the stuff you are talking about) and I want to learn more.
Depending on the size of your MH, you might save in the long run on energy costs, you won't have to run a chiller (if you do), nor will fans, if any, need to be run. Not to mention LEDs are extremely efficient at turning electrical energy into light. MH creates a massive amount of heat as well, with heat being energy, you can see what is basically wasted energy.
What you'll need to know for LEDs, basic electrical knowledge what voltage, current, and resistance is. It's a good idea to know Ohm's Law, Kirchoffs Junction and Loop Laws, etc. etc.
You'll always want to 100% understand the equipment with which your working, this is extremely important with electrical work as you have the ability to start a fire.
However, with LEDs, it's usually unlikely because the extremely small (compared to other lighting options) voltage and current draw from LEDs, it's hard to actually start a fire if everything is wired correctly with built-in safeties -- fuses, breakers, and/or thermal protection.
LEDs are engineered to output light in a certain spectrum, so yes, you can match the wavelengths of the bulbs to the needs of your livestock. So you can alternate color temps/wavelengths 420nm, 465nm, 6500K, 10000K, and 14000K (i've seen ads, but never proof of LED in this spectrum).
You can get LEDs in many different specificaitions, from fractions of a watt, up through 10 watts per piece.
The real specs. that matter in lighting are the penetration ability into water, lumens (or flux).
there are a ton of electronics hobbiest forums and magazines out there. It's invaluable to know how all of this stuff works, I garauntee it will save you money time and headache in all aspects of life.