How (or what is the best way) to raise and / or separate an LED from the PCB?
If I were doing this I would either look for a light pipe, or just make a small through-hole pcb with footprints for the led, and for some long 0.1 pitch headers that would go down to the main PCB.

You can get a few hundred small custom PCBs for next to nothing these days.

The only downside I can see for this solution is that it will probably require a jig during soldering to get the right stand-off height.