With the 2.5L engine, it wouldn't (shouldn't) have the 3.07, it should be 4.11. That can be verified by finding the ratio that is embossed into the steel tag between two bolts at the 9 o'clock position of your differential cover.
Regarding the TB, I'm in agreement with Jp magazine that you won't notice a difference running the 4.0L TB on your 2.5L. They tried it recently and didn't notice a thing.
With your 4.11 gearing, the only worthwhile gearing to go to is 4.88 but that would be a pretty low ratio for only 31" tires. Personally, I wouldn't regear for 31" tires, it's expensive and it's too easy to go too low (of a ratio) with a tire that small.
If you were going to 33" tires I'd strongly recommend that 4.88 ratio. If you did have lower gearing installed, it's typically pretty close to $1200 total for both axles including all parts and labor.