My goodness, Schala's gonna be a force to reckon with. I don't have too many suggestions, regarding the tech list--coming up with these final triple techs is gonna be a challenge.
And I think the reason they wanted to pick someone other than Golem Overlord is so we wouldn't have to come up with a way for the creature to have randomly appeared and disappeared: you bring in some random Golem, people already see the connection, you kill it off and no harms done to the canon.
EDIT: You know what...I don't know how much sense it would make if a Golem was behind all this instead of Mecha-Dalton...I mean, it's a very man-made-sounding problem. If the disease/plague/pestilence just randomly occurred and some neerdowells took advantage of the situation, for whatever reason, and the Golem just happened to another goon for you to fight, then maybe its inclusion could make sense, otherwise it needs to be some kind of humanoid problem.
For instance, the plague randomly occurs naturally, but these Daltonites use it as an attempt to engineer fear and control over the already disheveled masses. There is no known cure, but Schala or someone comes up with something, Crono and co. have to go fight some baddies and do a little fetch quest, and voila a cure is made, and the hold of the Daltonites is eradicated.
Blah, I'll leave the ideas up to you.