There has been a lot of discussion over the years about what mods add power and how they do it.
Without a tune nothing has a lasting impact.
With a tune the consensus seems to be
high flow cat = 16 HP plus or minus
The stock charge air cooler is fine for the factory tune unless you are using a lot of power in hot weather.
An after market charge air cooler does not add HP but also does not limit power so it allows the car to be driven harder on a hot day and enables other power adding components to do their job.
Cat back exhausts are mostly cosmetic. The factory exhaust system does not inhibit power until you see significant gains.
The factory charge tubes cause turbulence at higher RPMs which acts to limit power production at those same higher RPMs. After market charge tubes, in my experience, do not ADD power but they allow the tuned car to continue to produce peak power for a broader RPM range which translates to a lot more area under the power curve.
There are a few members who SWEAR that the after market charge tubes actually add power. I am not of that opinion but in the past they have been adamant in these claims.
There are a number of threads that suggest that at about 400 HP the manual transmissions start to have reliability issues. I recommend that you do some research and make up your own mind.
In response to the comment above about the IC failing, there are basically two failure modes. One is a manufacturing problem that resulted in ballooning of the intercooler due to improper manufacturing. The second failure was identified on cars that had the GMPP or an after market tune installed. The intercooler structure failed resulting in cracks and leaking. These were very difficult to find but caused a lot of issues on a very small number of cars. They were finally found by listening to the IC as the car was started when you could hear the leak during the first few seconds of the startup.
I don't expect to see power gains from upgrading the tubing, it's just something that I think looks nice and future-proofs against any plans I have down the line. The intake I feel needs upgraded due to the plastic check valve, and since mine is trashed anyway I don't have a problem with it.
The intercooler needs replaced, it's not ballooned the way that I've seen pictures of, but it would not surprise me if it was cracked or holed. The entire piece is bent into an arc around the bottom bracket that holds the tube underneath it, like it was driven onto a rock or something. I'm definitely replacing that and ordering new couplers, since those were a failure point previously. Something weird though, I already have T-bolt clamps on the stock couplers, but some of them are too big, like they were ordered for an aftermarket cooler with 2.5" flanges. That's where I ran into problems last time.
I know I need a tune but I'm not really near any of the big names around the forum, is a canned tune worth it? Could I go to any old dyno shop in the area and get adequate results? Or is it worth making the time to take a trip out?
Lastly, I know my transmission is still a weak point, but I've looked around for an upgrade path and haven't seen one. Either there's the pricey T56 upgrade or a swap to an Aisin 6 speed, which I seem to understand is more of a sidegrade than anything and doesn't improve reliability. Am I missing a third option there?