The AP is going to be one of the best investments you make for the car.
If you pick one up from a tuner like
@brian60 said they'll include their tuning service with it which is great.
Go with a lifetime tune for sure since you're mostly stock? This way your car will perform the best it can with the upgrades it has and you can revise your tune as you continue to modify.
The Depo intercooler is a good intercooler for sure, it will handle the power you're looking to put down unless you're going to break the 500+ HP range then you might want to look for something beefier like their 5.5" but even then it might be overkill.
As for the charge pipes your factory pipes are fine even into the big turbo range. The only benefit you'll get is you can put the hard pipes on and locate a universal BOV onto the cold side (factory cold pipe is rubber, hot pipe is steel)
As for what
@TS13FST stated with the mountune kit, I would be leary of that kit if you decide you want to go more of a custom kit. The mountune upgrade bundle is great but then you're stuck. The kit they sell doesn't allow you to have the AP flashed after the initial kit.
If you end up going big turbo you'll have to get another AP as it can't be modified once used or unmarried and sold later as Mountune has some other system they use even though it looks like a generic AP.
Best of luck! a lot of great info in these forums. Enjoy the car!