If you don't want to have to do anything complicated you could simply wire the LEDs in parallel with one resistor per LED.
Make an array board out of plastic with holes drilled in the spacing/pattern you want.
Then you can solder the negative leads all together, or make separate circuits and lighting patterns for running and braking. I did the latter because it was easier.
Or if you want dual intensity you could simply wire the running light circuit to deliver a slightly crippled supply to power to the array, then have the braking circuit supply full voltage.
You can buy LEDs (often with resistors) in bulk lots of 50, 10, or 1000 factory direct through eBay.
http://stores.ebay.com/Chi-Wing-LED-...QQftidZ2QQtZkm
6000mcd LEDs will be more than bright enough for brake lights.