All good man, it's a common issue. Kit looks good, there are always a few things to sort out. That bit off the neck heel isn't really a problem, you can just tidy it up a bit if it bothers you. A gap between that and the back of the pick up route is completely normal. You may find the neck has to come further out of the body to ensure the scale length is right. That will probably help with the gap you have between the bottom of the heel and the cavity as well, I don't think the neck is in the right spot atm.
You will need to temporarily install the bridge (don't push the post receivers in, just tape up around the posts or use a bit of hose or something so you can sit it in the right spot) and then measure from the inside of the nut to the bridge to find the right neck placement. Is it a fender scale length? If so you want the bridge to be ~648mm from the nut. Usually the high 'e' is closest to this measurement with the rest of the strings ending up slightly longer for intonation. So move the neck so that you have adjustment available for the thicker strings to go back toward the tailpiece.
Looking forward to seeing where you go with it.
EDIT: just looked and i can see its the Gibson scale so 628mm from inside of nut to bridge saddles.
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