Welcome WeTheNorth.

Sonic makes some great points above and has built more PBG kits than I so offers some good insight. Most of my building has been non-PBG non-kit.
I also agree the TL or ST kits are good starter builds. Especially for learning and understanding the geometry of guitars and what makes the difference between a guitar that's just playable, and a guitar that plays great.

As for upgrades, SM nailed it with saying that, at minimum, the plastic nut has to go. From what I've seen the kit tuners have been quite good and are not what I would say require immediate replacement (like the nut). The only shortcoming I might note on the bridges, would be the stock saddles. I'm not a fan of cast metal saddles on anything, that's merely my opinion.

Also, I might add that doing a string-through with the TL is completely doable with a hand-held drill, but does pose its challenges. Do heaps of research about making a template or jig (here and elsewhere) and take your time when it comes to the actual drilling part. Like always "measure twice (or ten times) and cut (or drill) once!".

For pickups, if your an experienced player and know exactly what you like in a pickup, get what you want and do it as part of the initial build. FWIW, I haven't used any of the included pickups with my my two PBG kits, but I tend to have very specific ideas on my pickups. BTW, you can't go wrong with any of the Toneriders IMO.

Post something once you've decided on a kit and there's heap of folk here to offer good advice once you get building.
Look forward to seeing what happens next!

Cheers,
Mick