1. What is the major difference between a 3mm and 5mm (more light? Last longer??).
The difference is just the size. Depending on your application you may need a smaller or larger light.
2. What made you chose 5900 mcd (and what is mdc?!) and not the smaller or bigger numbers?
MCD is an abbreviation for millicandles. It's similar to candlelights which is what flashlights and the like are measured in. Many places will give a lumens number but that only measures the amount of reflective light. MCD is a better way to measure the overall brightness of a light. LSDiodes.com sells extremely bright LED's, which many have a warning for possible eye damage if you look directly into them for periods of time. (kind of cool...lol) They have some white leds that are rated at 11000mcd. BTW...I wouldn't go as bright as possible on LED's (higher mcd number) for an aquarium. I had these laying around the house and thought that they would work well. The higher the mcd the deeper the light will penetrate.
3. What would have to be done to make the "pvc strip cut in half" work mentioned after this post?
First you would need to geta piece of PVC that spans the length of your tank, make sure that it is white PVC and not grey. Then with a table saw or a bandsaw you would need to cut it in half, length wise, so that it looks like a really long U. You could either drill holes on one side and direct the light upwards into the U or you could drill the holes straight and just catch the other side. (IMO the first way would generate more light into the tank) Then you would need to determine how you plan to power the LEDs which will determine how you wire them as well. To make a moonlight you need to understand how to step-down a voltage using resistors to the required (forward voltage) voltage of the LED. Too much voltage will blow the LED's...too little and they won't light up.
4. Do you have to use the circuit board material (i.e. in the long strip set up)?
No you don't have to use a circuit board. I chose to in order to keep everything as 1 unit and to help keep the legs of the leds from touching. I also placed some di-electric grease on all exposed metal to keep them from rusting and corroding into the tank.
5. What does the resitor do (i.e. how/in what way does it 'protect')?
The resistor 'steps down' the incoming voltage. The powersupply that I was using was rated at 12vdc but when I cut the cord and checked the actual voltage it was at 15vdc (3vdc higher than anticipated). Each led that I used has a foward-voltage of 3.3vdc. (Series circuit is where each positive leg on the led is wired to the negative leg in front of it...so it looks like this in a schematic +-+-+-+- Parallel circuits is where each positive leg of the led is powered from the powersupply) When you wire the leds in series, each light will step the incoming power down by 3.3volts. So with a 12vdc powersupply each light is using 3.3volts of the powersupply. (hope I am making sense) If i ran them in parallel then each led would receive 12vdc, which is too much voltage.
Series Circuit
Parallel Circuit
Hopefully this answered your questions. LSDiodes.com has been one of the cheapest sites that I have found that carries LEDs that are this bright. Their not out to make a killing off of LED's like most companies and they try to keep their prices low.