Don't forget that scale length is a big deal on these builds.....they don't need to have neck pushed all the way in to the rear of routed neck pocket. On mine there was no room left for neck pickup mounting ring but the scale length is perfect. I could have moved neck 2mm to 3mm forward to accommodate neck PUP mounting ring but then it would never intonated properly.

Just need to slow down and thoroughly check everything before considering gluing the neck. The neck glue should do a pretty good job filling those gaps but agree with Simon to leave things sit for a bit longer to see if there is any more expansion or contraction to contend with.

Cheers, Waz.