No question I'd pull the frets and re-fret. With all the work put into the guitar I wouldn't compromise on the playability and longevity (if you have to do some heavy fret leveling now, it's just going to be that much sooner the guitar needs a re-fret anyway). A couple hours of work and you can get the frets pulled, the fingerboard re-leveled, and ready for new frets.
Are you hammering or pressing frets in?
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