I'd suggest that shards auto-upgrade when the appropiate tech is researched, or the mana bonus is automatically given per shard.
It's kinda micromanagement hell right now when you have a large empire and a ton of shards.
That said, with this change I'd suggest the following:
Shard harvesting needed to harvest shards at +1
+2 shards comes with another magic tech, possibly rituals or a new tech (Shard Focusing?)