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Hello -
While I've not put a flag on a Mini roof, I have done exactly
the same type of installation many, many times in my 16+
years in the sign business.
I installed the dealer UJ myself ($129 at Classic MINI) on my hardtop. It was more difficult than the factory instructions make it sound. I spent about 2.5 hours and used a hair dryer on a couple of spots. I would not recommend a heat gun -- a hair dryer is plenty hot. I think a sunroof-only job would be trivial to adhere and tedious to trim.
MotorWorf - If your looking for a perforated pre-cut sunroof piece we have it. We can provide this in white or black and have some other designs in the works. Shoot me an e-mail and I can give you more details. Matt@cooperflags.com