Yeah if the inserts are too polished the clear doesn't adhere well. At least that's what I've seen & heard. It's either a decent sanding & clear, or multiple finer grit wet sanding to a shine. Sounds like you should be fine though.
My best advice is get an extra set of hands for the hardtop install. One guy to hold it up, the other to peel the sticker & supervise the placement. Use your air compressor & tack cloth to get every speck of dust off of there before laying it down. Just take your time with placement & nitpick every insert to make sure you have it lined up just right, then clamp one end in place firmly & take a deep breath before starting. It really wasn't that hard though.
You'll also want to take a good look at the shooter lane. Depending how you sanded it, the groove in the wood may be longer than the cutout in the hardtop shooter lane. You may want to cut it accordingly to your shooter groove length. I was too afraid to cut mine, but the difference hasn't affected my plunges at all. I'm pretty sure all the hardtop grooves are cut shorter than the wood groove