After a full run through of KSM, you are able to reach Mameema, the daughter of storms.
Bring her a seal (from Ys) of the stat you wish to lower and a scroll (from Ys) of the stat you wish to increase (for example a seal of spirit and a scroll of constitution would lower your base spirit by 1 and raise your base con by 1).
You may repeat this a max of 3 times.