I'm no expert but have a few builds in the done tray so I'll offer a few tid-bits
My general order of upgrade priority on kits is as follows...
1/ Tuners. 2/ Nut. 3/ Pickups. 4/ Bridge. 5/ Electronics.
As my IB-1Q build proves (due to locking nut and Floyd bridge) it's not a hard and fast rule, yet there are reasons based on experience.
1/ Tuners... There is nothing more disparaging than tuning a guitar and then have to re-tune two seconds latter because of tuner slack. Three or Four more tuning attempts latter and then the tuner gears start to bind up. It's never an issue with quality tuners. For ease and confidence in tuning your wonderful build or partscaster a good set of quality tuners are a God send. Pretty well every PBG kit that I've purchased was ordered with a set of upgrade Grovers with the exceptions being those builds where I got Klusons or Wilkinsons or Fender from elsewhere.
2/ Nut... Plastic nuts are simply annoying. Yeah, they are able to be used to tune a guitar for the first time, and may work okay for a while, but the tuning stability and the "Ping!" that you get when you use your Whamy bar and the subsequent angst will have you soon wishing for better. Be it TUSQ or something made from bone it matters little as both are far better than the dreaded plastic.
3/ Pickups... I can't say any of the kit supplied pickups are bad as the few I have used in my builds have been quite awesome. For me it's more of having a known starting point. Kit pickups for the most part are an unknown quantity and brand name pickups frequently have a history that can to various levels be tracked on various websites and places like YouTube. The issue is what goes into their DNA. Knowing what magnets are in them and reported balance/performance/tone helps in making decisions on what a 2nd pickup upgrade may consist of if it ever happens. I will say here the only choice disappointments I've had so far has been a set of SD rails in a partscaster Strat build and a set of AC2 Toneriders in my ES-1TL build so both are candidates for a 2nd round on the pickup upgrade bench. Two outstanding first choices of note (maybe I'm simply getting better at it) were the Dimarzio IBZ's in the IB-1Q build and the Entwhisle AT52 set in the TLA-12 build. I'll include that I've been impressed with some choices like Yibuy P90's in a LP build and some Chinese Alnico 5 beasts that found their way into a SGM-1 build and the passive EMG select in the RCM-4F build so all is not lost in the forest of guitars I have.
4/ Bridge... The biggest reason I have here is the ease of doing a guitar setup with better quality parts. For the most part I'll use the kit parts unless I have outstanding reasons to change them. So far it has been things like adding a Bigsby or switching to a different size trem block that instigated most changes though switching from Black to Chrome hardware was the reason on one other build.
5/ Electronics... For me there is only one reason to upgrade the other electronic parts in any build and that's reliability. Cheap parts will work and do the job well, possibly for many many years, however quality parts will do the job reliably for many years more. Quality parts are a must for a working/giging guitar that does shows 6 nights a week, though cheap parts make economic sense for a guitar build that only gets played a few times a year.
As for the other bits like straplocks I'll take a pass. Standard kit hardware for me is more often than not just fine...
I hope my comments make sense to some... Everyone’s mileage will vary & everyone has different tastes...