There's no metamagic feat to boost caster level. The heightening on the spell to 6th level is essentially free. You could either do a 3rd-level slot or a 6th-level slot with no difference from your perspective. It gives the DC +3, not that it matters much but you never know. The save on the spell is relevant. He's either fatigued or exhausted.
Ah, and now I understand your point. However, I don't think the same effect stacks. You can't use two rays to guarantee exhaustion. I had not paid close attention to the past round otherwise I would've mentioned it. You'd be better off with the maximized, empowered ray of enfeeblement.