LED setup help

Now that my skills are a bit better I want to revisit Project: Green Lights lights.

Before I had the bottom light (green one) hooked up to the HDD indicator light and that proved to be bad. The LEDs were nowhere near bright enough.

I would like to make something that has the 3 lights (red, yellow and green) alternate. But I want them to be bright. I have the plexi needed I just need to know how to wire it and what to use. I want them to project light, not illuminate the plexi.

Here is what the the plexi behind the tubes looks like. I have about 1/2"-3/4" space to work with.

This is what the current setup looks like... no projection of light.

How can I make this work? What size LEDs to use? Resistors? How to wire it to a molex connector?

Cheers and thanks for the help.