For anybody who had/will have the same question:
You get Sun Stones later in the game, after beating the Touhou Leage 4; all the information you gave is correct, you can buy them on the 2nd Seafom Island at the shop.
The are only applicable at the normal (after Chibi, before Ex/Final) evolution level, at least its like this for Reisen, which evolves to Final Reisen (as opposed to EReisen through leveling up); the sprite is way cooler and she has a higher SpAttack...
All information given is for the Merry Version 1.5