I had the same problem when I orderd in 2011. I wanted the more basic car with cloth seats, but ended up getting the Premium package because I wanted some of what that included, but none of it was available as stand-alone options, which was unfortunate, as there used to be a stand-alone interior upgrade package for about $450 when my parents bought their 2005 base GT, that somewhere between then an now got dropped.
The Brembo package and the gear options are about all you can get on a base trim GT. Performance wise, those are about it for factory options on any GT trim. The shaker 500 stereo is only available (and standard) with the premium trim, which also includes a power seat, satellite radio, interior/dash material upgrade, leather seats, leather wrapped steering wheel, extra gauges with mycolor, a usb port, Sync, and a few other small trim pieces.
The C/S grille piece is something you would have to get as a dealer or aftermarket accessory given what you want. You can't get both the Brembo package and the C/S package together. The C/S package is also only available with the premium trim, and on it's own, is a pretty expensive option, I think.
So ultimately, you'll have to decide what tradeoffs to make. If you are willing to give up the Shaker 500 system, you can get cloth seats, the Brembos, and 3.73 gears from the factory with the base trim, and then add the C/S grille as an accessory. So equipped, a base GT will sticker for around $32K, which after rebates and incentives, you should be able to get it for about $27-28K give or take (plus tax+ the aftermarket grille) with a good deal and X-plan pricing (join Mustang Club of America, and you qualify for that). The only downside is the interior is a bit bare on the base trim.
If you want a sound system upgrade, you either have to spring for the Premium package for the Shaker 500 (which will add the whole list about and $3700 to the sticker), or get an aftermarket system installed somewhere.