This one is a bit custom, and very specific, I should assume. I am eventually going turbo (TD05-16G), but for a while, at least, I will be naturally aspirated. It's stock right now. I mean bone stock. I mean stock intake stock. I was sort of planning on a throttle body being my first mod, after an intake. Is this a good first or second mod? After that, I figured I'd work a 3" catback into the equation. In any event, here's my question.

I've read a lot of stuff about throttle bodies. From what I hear, the intake manifold inlet is 52mm. The stock throttle body bottlenecks down to 46mm. The two options, from what I can see, are 55mm and 60mm. Both of these are obviously larger than the intake manifold intake. How badly will this screw up laminar flow? Will I lose power? Will I gain power? From what I can tell, the stock manifold can't even be bored to 60mm, without adding metal, which I won't be doing.

My question is, in terms of driveability, and power both stock and with at turbo, what is my best choice? 55mm? 60mm? Should I go with the modern performance throttle body?

It seems like this question has been asked a thousand times, but I never got the answer I was looking for,

The Modern Performance 60mm TB is a great upgrade. Knowing your overall plan, it would be the best option in the long run, but definately not the least expensive option. If you weren't going to boost, I'd say go with a bored stocker or the Jeep TB mod for more flow.
At this point in the game, you aren't adding a lot more air flow naturally, even with the larger TB opening... You won't come close to experiencing the gains until you go turbo. I would start collecting the components you'll need for boost, consider replacing your Headgasket with a nice MLS one and upgrading to ARP headstuds. Get an UDP as well. Those are my opinions on your next "mods" along with a nice free flowing catback exhaust.
Having a larger TB opening than intake manifold opening may cause some slight flow issues, since air will be effectively hitting a wall after going throught the TB. The Stock intake can be ported larger without adding material. My Stocker (shown in my sig) is ported slightly larger than my 60mm TB opening for a smooth transition. Just gasket match the TB, then put it on the Intake and see what material you can remove. Obviously make sure the intake is off the car so as not to drop metal into you cylinders...but it should be a mod you can do yourself.

Jepp TB. Cheap and good.

So should I get an intake, considering I won't be boosting for at least 6 months? I've actually decided now to go with the Tsudo N1 3" catback for the GS-T. Hopefully it won't destroy my low end torque.

I bored my intake to 60MM.......I didnt have an issue and I didnt add metal either.

if you're willing to do a little work the Jeep TB mod can't be beat. you're not gonna lose anything for running a bigger TB while you're still NA. Actual HP gains will be negligible but you will notice a nice difference in throttle response.

if you want 60mm get the auto trans Jeep 4.0 throttle body, the manual trans unit is only 55mm

Well, today I went at the stocker with some carb cleaner. It was dirty enough that my fuel trims weren't right. I had to reset my ecu in order to get it to idle properly. At least 6 mm of growth on the plate and the walls past the plate. It's polished now though. Throttle response is off the chain. Makes me wonder how a 60mm would be?

You will love a 60mm.

Best mod ive ever done.

60mm > UDP > Lightweight wheels are the best ones IMO.