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Unfortunately with most of the aftermarket hoods there are huge issues with fitment and large panel gaps. If there was a aftermarket hood manufacturer that was consistent in producing hoods that fit well and had factory like gaps with the fenders and bumper I would give up with the OEM hood and go aftermarket.
I have a Black 2006 Convertible GT, ( Garage Kept, with only 66K ) and mine has the Bubbling Under the hood and now coming through at the front Lip of the hood. Fords Quality control is **** !!
Found bubbles on the leading edge of the hood on my 2012 V6. Didn't notice them when I detailed and waxed last spring, but I honestly could have missed them because of the angle.
I called my dealer about the issue today and they won't even look at the car. It has ~22k mi on it, but it's been more then 3 years since purchase. PremiumCare Warranty I purchased with it "doesn't cover paint". They referred me to their body shop (a 3rd party) and gave me the number.
It looks like only these two spots on the passenger side right now. Pretty lame if you ask me. Trying to figure out my options now...
This isn't a great picture of it, I'll get a better one later:
I had it on my '14 V6 and Ford did pay to fix it. The owner of the body shop said that chances are good that it would come back. The only full proof fix was to get a new hood. Or I'm my case, get rid of the car and get a '15 GT!!!