I had a similar problem with the exact same kit. The front half of my neck pocket sat higher than the back, causing a gap. Careful sanding for almost an hour was what cured it, though they advise you NOT to sand the pocket. For me I had no other choice. I’m sure others will chip in, but you could also place a thin piece of MDF or something under the heel to level things out. Just my 2 cents.
I'd leave it for a few days if its done any air travel, as the wood can expand or contract with temperature and humidity changes. So let it settle down indoors for a while and you may find things are different. You can of course sand any machine marks off the edges and sand the top and back smooth in the meantime.
Then I'd rub chalk over the bottom of the neck heel, put it in the pocket and see from the chalk where it's touching and where it isn't. The bottom of the pocket/neck is where your strongest bit of gluing will occur (you'll clamp the neck down to the body, not to the sides of the pocket) so you'll want that join area to be as flat as possible. You can then sand down the chalky areas a bit, then repeat until you manage to get chalk pretty much all over the floor of the pocket.
You are almost bound to get some small cracks showing around the outside of the join, but they can be filled later as long as most of the neck is touching the bottom of the pocket.
Any serious gaps are best filled with bits of 0.6mm veneer (maple veneer is good for this).
Thank you Sachin and Simon for sharing your thoughts and experience on this. I'm in country Victoria, so the dry conditions may influence the wood. I'll give you're suggestions a try. i'll surely be sharing my progress.
The gap may get better or worse, or it may stay the same. But a few days wait should indicate which way is most likely and it's really not worth taking remedial action until it's settled down.
The only thing I'd add to Simon's suggestion would be once you've chalked it up, seat it in the pocket with a bit more than hand strength. I used a light tap with a rubber mallet and s clamp. These can be a little tight on the sides...