You can purchase LED spacers that are (effectively) x-shaped bottom parts with a flat disc on the top having two holes for the leads. The 'x' part is closest to the PCB/track but gives access to the copper tracks as the leads are 'exposed' down the channels formed by the 'x'....

Not sure of the available heights but you could use a standard spacer on TOP of the x-shaped one.....

Farnell do these x-shapes (amongst others) - their part number is 1325971 - check their website.