You can't even buy the parts for $3,500, so I have no idea where you're getting that figure!
FRPP has two different blowers available for the 2005-2010 Mustang GT's - both made by Whipple. Both are dealer-installed and can be included in the financing of the vehicle.
I work at a Ford dealership that has already done a couple of blower installs.
The first one is non-intercooled and rated at 400 flywheel hp. Depending on the finish you choose (black or polished) and the labor rate of the dealership, expect to pay between $6,500 and $7,500. Your factory powertrain warrany is reduced to 12 months or 12,000 miles, whichever comes first.
The other blower is intercooled and rated at 500 or 550 flywheel hp (depending on application). Expect to pay about $1,500 to $2,000 more for this kit over the 400 hp kit (parts and labor are both higher). That means it'll likely cost about $8K to $9K for this blower to be installed at a typical Ford dealership. This blower comes with absolutely no powertrain warranty and is not suggested for automatic transmissions.
Not all dealers will be willing and/or able to install these. And pricing can vary a bit from dealer to dealer, but the ranges I quoted above should net the dealers a couple hundred bucks in profit, so there's not a lot of discounting available.
While it's cool to say that your new supercharged GT is "stock" because it came with a FRPP designed, dealer installed blower, there are actually lots of good aftermarket blowers on the market for similar or less money.