Your Thoughts

I'd say these are the best mods to do for you.

1. Xcal3 custom tuned by someone like VMPTuning.com
2. C&L or JLT Cold Air Intake
3. Steeda UDPs
4. Steeda CMCVs

I'm running these mods with a Pypes O/R X and Magnaflow Magnapacks and put down 304 rwhp and 316 rwtq on 93 octane with 10% Ethanol. Justin at VMP Tuning can tune Mustangs and even F150s like no other. I've been running his tunes on three Fords and couldn't be happier.

CAI/tune is the biggest bang for your buck. Just make sure you get a CAI that is big enough to require a tune. The ones that don't require a tune will not flow anywhere near as much as the ones that do. Personally, I like the Steeda/Ford Racing CAI. It was designed alongside Ford engineers, and it comes stock on the Shelby GT's and I think the Bullit's, too.

At set of gears does wonders, too.

Also, for your consideration check out BamaChips and BrenSpeed. They have great CAI/tune package deals, and their custom tunes are the most popular with S197 owners. BC sells Predator and SCT, BS sells SCT only.
Personally, I use the Predator with BC 93 Race tune, and I've never looked back.

wow, 600 installed INCLUDING PARTS is the norm. some less, some more, but definitely not that high

Gear swaps (parts & labor) tend to run anywhere between $600-$1,000 around the Seattle area (I've called a ton of places and done a bunch of gear swaps on my cars. I got my 4.10's done in my 07 GT for under $500 (parts & labor) after shopping a LOT to find the right deal from a place I could trust.

CAI & Tune is definitely the biggest bang for the buck on 2005+ GT's, though. Gears are next, IMO. And any power adder is awesome, as budget allows.

Most mods in these cars require a tune, so that is implied. CAI is the first place to start, just the cheapest mod that gives good gains. After that, probably axle back, just for the sound not much power there. Then I would do LT's and an H/X-pipe, either off-road or high flow cats (personal choice), and with the LT's I would do the delete plates. And somewhere in hear new gears would help, but depending on your needs you may not want them. Underdrive pulleys are also a very common mod. All of these mods will increase gas mileage, with the exception of the gears which highway mileage. Now you could stop here...

For the real motor-head here is your first major choice, FI or NA. FI is easy enough, buy your supercharger of choice (or turbo for those of you with that wild hair). My personal favorite, for its co aesthetic and power, is the saleen supershaker (their supercharger that is combined with the mach-1 shaker). At some point you may want heads and cams.

NA is a bit trickier. Don't bother with the delete plates, cus the new intakes are going to hit the market, if you use a turbo or centrifugal supercharger this would also be a good mod. Now you need to decide who you want to port your heads and which cam you want. The cam market is starting to look pretty good, so now's a decent time start these upgrades. Personally, I like Livernois motorsports, everything I read and hear about them is the best.

Now, with either NA or FI you're going to want to look at a new bottom end (since everything else is about done). For FI, you can do a stroker or not, either way, and some big dish pistons for lower compression to let you run more boost. For NA, again a stroker is an option but some high-compression pistons really help power numbers everywhere, it should also help gas mileage. At that point you're pretty much done, with something like 10k+ in your engine!!

This, of course, doesn't even touch the suspension, which is just as important.
Dan