I totally get where you are coming from Aaron. I bought my ST with the same intentions, but after reading up about flexi pipes and induction kits I thought sod it. FYI an induction kit can easily be removed it you have any warrenty work to be done. For servicing.. as Pinkrinse has said on numerous occasions, you are PAYING them to service it, they can't be funny with you about it. When you lose out on mods is when something goes wrong with the car and they have something to blame it on (i.e. engine is getting to my air or some gem like that...). Flexi pipe is a stealth mod

I can't see that a Ford garage would even notice that - the guy @ pumaspeed said pretty much the same thing to me when I was chatting to him about it.
I've had a Green Cotton induction kit (boxed and in the garage now) and a K&N57i. The K&N57i is a superior product.. doesn't sound as loud, but fit wise its much better (performance wise, can't say I noticed much difference). Let me just say, that the flexi pipe + the k&n57i is definately worth while imo. My car is a lot more eager to perform now, I don't notice that 5,000 rpm "im going to explode" feeling I did before with the car.
Theres no great increase in power from a cat back, so im keeping mine standard for the time being as I can't see the point of spending a few hundred quid at this time. As for the lowering springs, thats one I've also considered. Apparently *IF* my local Ford dealer fits them, it will keep my warrenty intact... but i need to confirm that, and also get a price.
I've read about people having their car lowered, and then having to pay out a few hundred quid for a CV joint because its gone and Ford say its down to the springs. I'm still undecided on this mod, and am leaning towards leaving the car standard ride height (but then i've never been one for lowered cars, im only interested if it makes the handling better).
Anyway, good luck with it - but from my own personal experience, get the K&N57i and a flexi pipe... Also I was very happy with Pumaspeed, he fit my flexi pipe ver quickly and was friendly and helpful. The K&N57i you should just do yourself its not a massive job (tbh you can do the flexi yourself, but you will need a ramp or axle stands).