3.1.4 will run on a 3.1 ROM at the expense of some RAM - it has to kick in some module updates just like 3.9. There are rumors that 3.2 is imminent, so you may want to wait for that instead of going for 3.1.4.
That said, any of 3.1, 3.9, or 3.1.4 are good choices. I think you're right that 3.9 makes the most sense for now, especially since you have it on hand. 3.1.4 includes most of the improvements from 3.9, but not all of them, but does have additional bugfixes and improvements of its own. Ultimately, though, there's no wrong answer here.