I'd still wait a couple more days before doing anything with the neck and pocket.
Clamping the neck in hard, if the neck is slightly too big in places, will force the pocket wood out slightly and so could enlarge any gaps. Hard to tell exactly what's happening if you aren't right next to the guitar in person. But there will be some gaps that a fine wood filler will fill.
Here's my EX build from the assembly point onwards (ignoring the selector switch routing). It hasn't really moved on from the white nitro paint spray, as I need to wait for the weather to warm up so I can add some decals and then clear coat.
You can see that I had some fine gaps round the neck joint. I used a filler, then sanded everything smooth.
There are lots of build diaries here showing how people did their finishes, so I suggest that you read quite a few of them to see what others did and the results they obtained. Just ignore the ones using Dingotone as it's not available outside Australia.
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