Those ideas to combine crystals into clusters using synthesis are all far too cumbersome.
Can't use synergy for it, because crystals are a fuel source.
Using NPCs to convert is cumbersome too, since you can't use them when needed and usually require walking across Vana'diel.
That leaves us with an inventory item.
Crystal Fuser
Upon use, it will show the light crystal synth animation, and all stacks of 12 crystals in inventory are converted into 1 cluster.
Crystal Fuser could either be a non-charge item like Magian Spectacles, a 1/1 reusable like Portafurnace, or something like a 30/30 charged item that requires crafting skill to make (and thereby boost the economy.)
Crystal Fusers could be created by combining all 8 different clusters using synergy.