I would put opti-coat 2.0 on both before the CB install and on the CB itself. It will bond fine with the plastic and many clear bra installers have reported good results in regard to weathering when it comes to the bra.
As far as under the bra, I personally don't mind a little extra protection between the factor clear and the bra itself. I would not use anything other than a resin-based seal between the hood and the CB.
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