Hi and welcome to the forum woodpecker.
That is a very nice spalted maple top. I think leaving the pickguard off is a good choice.
I don't think the "No guard" is a problem for the neck. I would not lower the neck, or fill the gap.
I have completed a similar kit and the fretboard sat the same way! Check out:
https://www.buildyourownguitar.com.a...l=1#post222775.
The neck pickup route is small and designed so that no guard is needed there. A smaller pickguard or control plate could work.






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