I have a Cobb, FBO, custom tune and all that stuff. Here is what I know that might be useful for you. I think you made a good call with Cobb. It's the preferred platform overall and in case you ever want to go the custom tune route that's the platform the major tuners use.
As to OTS tunes - Stage 1 really wakes up the car, all that is required is a high flow air filter. I would assume you have one give the CAI, but if not AEF Pro Dry Part #31-10255 will work well.
Stage 2, however makes a BIG difference. The major power gains are there and with the intercooler and high flow air filter, you are ready.
Stage 3 was pulled from the market but it's not that big of an issue as the bulk of the power comes with Stage 2, the difference between Stage 2 and 3 is not that big. You don't have a down pipe, so you aren't ready for Stage 3 anyway which you knew.
Now to the Custom Tune - this is where I differ with most, I guess. Of course, there is no black and white answer that applies to all circumstances, because there never is with any issue with a few variables, but that does not mean that we can't draw some generally supportable conclusions and the conclusion is: You do not need a custom tune. That's the answer. You in particular do not as you haven't indicated that you want very ounce of power out of the car. If you want to play it safe, the load Stage 1 and stay with it and be happy. To me, the difference between stock and Stage 1 is huge when it comes to drivability, it's just a huge improvement. With a larger intercooler, you have a big safety margin built in by running Stage 1 vs Stage 2 and you could increase that even more by running Stage 1 91 and then run 93 octane in your car for an even larger safety margin.
Now for all the qualifiers.....Much of the push for a custom tune is supposed to be because it is "safer" because it's made "just for your car". I am not saying that's a lie, but in reality, I think that it's a bunch of fanboy nonsense made to sell custom tunes. "You need a custom tune, bro. Really need to pony up and join our club bro. You just ain't a man without a custom tune, bro." That's what I mean by fanboy

. It's rampant, don't fall for it. Are custom tunes safer than OTS, MAYBE, BUT highly doubtful and here is why. Assuming your car is not a lemon, does not already have mechanical problems, then you are almost certainly not any safer with a custom tune than an OTS tune AT THE SAME POWER LEVELS. It's common sense. No company would build a device like Cobb and spend the millions of dollars behind it, without building in safeguards and those safeguards apply to all vehicles that are mechanically sound and running the CORRECT MODS. Run a tune without the correct mods in place? OTS tune blows engine. Fault? The idiot who loaded a tune without the right mods in place. Not the tunes' fault. So is a custom tune worth getting? Of course it is, IF you are pushing high power levels and trying to squeeze all you can out of the setup. Otherwise, just have the correct mods in place and load the correct OTS tune and be happy. Afterall, you have a testing device in the palm of your hand - the Cobb Access Port!!! Use it and monitor your car!!!! If you are seeing high corrections to ignition timing, frequent corrections to ignition timing, persistent knock counts, you have an issue using the OTS tune which is likely an issue with your car itself that needs to be corrected, but the tune definitively needs to be pulled until you figure it out. I say this because I have run the stock tune and all OTS tunes and the custom tune and monitored them all my car runs fine on any of them without any issues with knock and timing correction. The difference is that on the custom tune, the power band is wider, comes on sooner, and I develop more torque overall, but not a huge amount over Stage 3 OTS and all of that indicates nothing other than the custom tune is pushing my car HARDER and exposing it to MORE risk than the OTS map and that at that power level its a really good idea to have a custom tune vs an OTS. More risk, more power. The OTS maps are less risk, less power, PROVIDED you have the