you are correct about air flow in and out of the engine. more air in means you need to keep it flowing through and out the exhaust. there are all kinds of bottle necks like you mentioned. not to mention more air means more fuel and the need for a re-tune. the ECU can handle some of this within its own parameters but can only do so much.
the ported TB doesn't require a tune as it's only function is to help with air flow velocity. by porting the outer edges, there is a smoother transition from the CAI tube to the TB itself. it also creates more of a venturi effect which helps increase the rate at which the plenum can refill after you smash the peddle...hence why it improves throttle response.
the spacer (25mm) does a couple things. there is more science behind this but increasing the runner length shifts the TQ band to the left. it also isolates the air passing through the intake manifold from the engine heat (cooler air = denser air = more oxygen = more power).
a basic tune will cover mods that increase air intake volume (like a CAI) and adjust fuel trims to meet those requirements. i could be wrong, but i don't believe there is much to tune for on the exhaust side. generally, headers are tuned to produce optimum power for the motor within a certain RPM range. primary diameter and length, and then collector length. ex: longer collector is beneficial for mid range TQ. the more advanced tuning changes timing, AFR's, fuel tables, fuel injector pulse, etc...
but at what point do you sacrifice daily drive ability with maximum HP or dumping $$$$ to build out the motor? ...sorry, off topic. there are a lot of things that can be done to increase HP...but once you start reaching the limitations of the motor itself (assuming you aren't physically changing the internal dimensions of the motor) the mods that you add have a very limited addition to the final HP output.
EX:
MOD's claimed HP gain:
CAI = 15
LT Headers = 30
Insulator = 20
--------------------
total HP gain = 65 (WRONG!)
BBK LT headers claim a 33 HP. but that gain is at 5500 RPM (max HP 255-stock, 273-headers) max gain is really only 18HP
Injen CAI claim a gain of ??? not sure but its around 15HP. independent testing showed 17max...but in what RPM range is that gain?
-what if they both share the same RPM range for their claimed gain?
even with a gain of 18HP from headers and 17HP from CAI, your overall HP gain will not be 35HP. it will be a mash up of the two and hopefully net you something close to 22-25HP overall IF your lucky. not every mod adds HP, some just improve functionality and driveability to suit your needs. others do add HP and work together as a collective to improve overall output, but their output is more of an average vs a total of the sum.
not trying to insult your intelligence, just trying to explain how some things work and why.
