The SD schematic is confusing and doesn't show a HC4050 component as is in my schematics thats why I was still confused.
My ICSP header should still work, I just have the pins in a different order, which doesn't matter as long as they are connected to where they're suppose to go (GND -> GND, MOSI-> MOSI).
Here's the new LED wiring :
copied from the Sparkfun link you posted.
-Harvey