Go with 4.10s, best decision I ever made so far with my car. MPG only went down by two on the highway (I get about 24 MPG now) but my SMG (smiles per gallon) shot up BIG time!
And to the guy who said 4.10s would be way too much for a manual, especially a Shelby, all the Shelby GT has for added performance compared to a GT is a CAI so I dont know what you're talking about when you say "especially a Shelby." Although it does means he's going to have more fun with his 4.10s, that's what!
You'll hear some people say you have no first gear with 4.10s but I beg to differ, I've had no problems with first at all taking off or shifting and after a while I cant even tell the difference just driving, although from 3.55s to 4.10s, you can tell a difference with first right after getting the new gears installed. But honestly, you get used to it in a day, adapt, and use first gear like you did before. It just climbs up the RPMs a little faster, it's not that big of a deal like some people make it.
I've also found out that most people who say that there's no first gear with 4.10s, are usually the ones who dont even have 4.10s in the first place. I'm sure some people do, but every person I've asked so far "How do you know that there's no first gear?" dont even have them installed.
If you're worried about how high of RPMs you'll be at on the highway, I'm at 2500 RPMs at 70 (also gets you out of the drone zone if you have that problem), cant really tell much of a difference just cruising and the MPG still isnt bad at all, like I said, only a 2 MPG drop for a much more fun car. If you're worried about say, a quarter mile time, you'll top out of 4th gear around 120. And think of it this way, you'll have to push serious HP to get past 120, the new '13 GT500 finished the quarter mile going 125, so that should tell you something. You'll be fine in the quarter mile too.
And as someone else said on here, about $300-$350 to install.
4.10s for N/A, 3.73s for FI. I'm going FI in the future but still went with 4.10s anyway because they're THAT much fun and THAT much worth the money.