1st, welcome to StangNet!!!
From my understanding, the rotating of the MAF only applies when you have an 'in the fender' air filter, and therefore a 90 degree bend in front of the MAF. And on the 02 on up GTs, there is no sampling tube like on previous models. The sensor is in the middle, so rotating it would not do much.
But the C&L is really not a good product. It simply tricks the computer and causes you to generally run leaner. Running leaner creates more power, but this is really unregulated with the C&L MAF - as I said, it's just tricking the ECC.
If you have no other mods and no computer chip, you're probably OK. But as natx808 said, the only way to really tell is with a wideband A/F ratio meter. Head to a local dyno, spend $50 bucks or so and see what they tell you. If you have your OEM MAF, take it along with you and see if you can swap it out (you'll need a torx bit to swap the electronics over) and test it both ways. We'd love to hear the results!!!
I had the C&L MAF on my 02 GT, but with my SCT leaning me out pretty far already, it was a recipe for detonation. Actually, it would very rarely ping with the C&L MAF, but honestly, swapping back to the OEM MAF seems to make more lower end power, more responsive. Plus it gives me more piece of mind. The OEM MAF is not a restriction...it is good for 400+ HP.
What year stang and what mods do you currently have? And what do you have planned?