Yes I've driven from stock to whipple. Really the only thing that turns me off on the 07-09 are the wheels which could be changed, and the two piece drive shaft. I've contemplated what the OP has before but think I'd regret it. If it wasn't a 13-14.
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never had any issues with my driveshaft. is that more of an issue if you have big power? i did replace it however with a 1 piece aluminum one since i got one for cheap.