Excruciate gradually increases your crit chance as it ticks down. With AF body, typically I've proc'd the crit within 5-10 seconds of hitting Excruciate, but without it, it's more of a crap-shoot.

I believe that Thundaga does more damage/MP the softer the target is. Once a target has high enough defense, Thundaga becomes grossly inefficient (the chief example that comes to mind is Chimera, in Cutter's Cry).

I'm honestly not totally clear on the INT vs. m.atk valuation. INT is extraordinarily significant on Thundara, and seems less valuable point-for-point on other spells, due to Thundara's inherent and massive m.atk bonus while used in combo. My general philosophy is that if Thundara is doing over 50% of your total damage during an encounter, you should rely more heavily on INT than m.atk. Really though, you're going to want to provide yourself with as many gear options as possible and adjust accordingly based on your targets and the nature of the encounter(s).