I think the gemspark enchanting system shouldn't be exclusive with experience enchanting, instead it should be a way to make your tools even better after enchanting.

The idea is as follows:
There will be a 'Gemspark Anointing' table, by using gemspark as fuel (Or maybe gemspark shards if you think is too costly), you can anoint a limited amount of gems to a tool/piece of armor, and depending on the gem and the tool/piece of armor you'll modify a different stat that the item gives to the player, maybe you could even anoint full gem blocks for an even stronger effect?