The only real restriction is the single-into-dual exhaust. That robs you of 8 HP, at least, according to Chrysler.
CAIs are just noisemakers on the Pentastar. A properly designed long ram might be worth 3-5 HP, if you can find one, but I don't think even Legmaker offers one anymore.
I use Diablosport tuners on my 5.7s, but they're no great shakes, performance-wise. I like them for tweaking shift points and the like. I'd be surprised if they add any real power on a stock engine.
As far as a gear swap, forget it. The whole point of the 8HP trans is the crazy low-cut first and second gears. If you swap to 3.90 or something similar, the cost-to-benefit ratio is very poor.
Exhaust and brakes are the only performance mods I'd ever consider on a 3.6, unless a blower is in your budget, and even then, I'd suggest stepping up to the 5.7 instead.