If I have the Merciful property on a weapon that I'm spellstriking with, does it make my spell damage non-lethal, too? My initial thought was no, but I guess it wouldn't really matter either way.
Your initial thought is correct. Merciful turns all the damage the weapon does into non-lethal. Anything else (flaming, shocking grasp) is damage in addition to the weapon damage and would not be effected.