That little gap under the heel isn't unusual, I had the same on my kit. Once clamped and glued if mostly closed up. I then did a coat of finish, let it dry, ran a bead of superglue along it, let it dry and recoated and it's fine.

When you are clamping for glue, be careful how much force you put on the heel as it is possible to move the break angle in that process, worth checking and double checking as you go before letting it fully cure and bond.

Personally I like the covered kit humbuckers and I have them in a number of guitars, so maybe see how they sound to you first. The pots won't need changing for different pickups, but you can always upgrade them as well to better quality ones. The kit ones are absolutely fine, but are likely to wear out and go crackley sooner. So I'd just stick with the kit stuff and see how you go.

There are loads and loads of options for upgrades, the Tonerider pickups that Pitbull offers are great bang for buck if you decide the kit ones don't do anything for you.