The below is my opinion based on my personal experience and reading the forums for the past 6 years. It is not universal truth and not everyone will agree with what I am about to say. But here you go.
Charge tubes don't add any HP. They can reduce the drop off at higher RPMs. The end result is quicker acceleration but not more power.
Larger intercooler does not add any HP, but there is evidence that on the track or for highly tuned or modified cars that generate a lot more heat can see some improvement. My personal experience is that going to a larger IC provided no impact but did empty my wallet and caused me to spend a day interfacing with the car.
The factory catback is efficient enough such that adding an after market catback does not provide any measurable improvement.
Adding a high flow cat, or removing your cat, does add torque and resultant horsepower on a tuned car. With the factory tune, the software will manage engine paramaters to bring the power back down to 260 ft pounds of torque.
Adding a cold air intake or a high flow filter element provides no measurable improvement in performance. There are cases documented of MAF contamination resulting from going to an oiled air cleaner element. Adding a CAI results in changed appearance and lots more noise.
Adding the GMPP tune preserves the factory warranty, provides an immediate HP and torque gain that will not affect longevity of the powertrain. Adding the GMPP tune will allow hardware upgrades that can add HP to do so. For example, adding the HF cat will yield an improvement in HP of about 16.
Doctor Dave put my car with the GMPP tune, high flow cat, Dejon IC, charge tubes, CAI and MF cat back on his dyno and with some tweaking measured 305 HP at the wheels. That is on the order of 350 fly wheel HP.
The factory 5 speed is generally considered to be reliable at power levels up to 400.
The factory axles are generally considered to be reliable at power levels up to about 450. With very sticky tires, at 450 HP you can
cause the axel splines to fail.
The factory automatic is good at power levels well above 400 hp.
There are two different types of rods. Sintered and non sintered. There have been a number of failures that suggest that as you approach power levels in the 400 and up range, there have been catastrophic failures of the sintered rods resulting from very short term events. A single short lean run can cause such a catastrophic failure and has done so.
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Part of the reason I went from the mods plus GMPP tune to the LS3 was my desire to keep my car long term and make sure it was very reliable. In my opinion going to power levels above the 350+ I was at would cost a lot and I was not happy with the resultant reliability / risk / cost analysis.
Having said all that, there are a lot of members who are very happy with the westers tune and in its various guises, it appears to be a good, stable product.