It's not an exact copy of an Explorer where the fretboard is at body level, but on the
EX-1 it does sit a bit higher. With the flatter neck angle used by the kit it need to be a bit higher in order to get the strings at the right height for the bridge.
Here's my
EX-1 when I'd just glued the neck on so you can see the height for comparison.
I would have waited a while after getting the kit before any neck sanding. The wood has been through a lot of different climatic conditions on its journey to you, and it tends to swell up slightly. Always best to leave it one or two weeks before making any decisions on how well it fits.
If it does become loose over time, you can always stick a piece of thin veneer to the side of the pocket and then sand that down until you get a tight fit again before glueing.