I'd move the G saddle forwards (towards the neck) so there's a couple of mm of thread poking out (it may well be in that position already). The G string will always intonate furthest forwards, and it will probably end up a couple of mm back from the scale length position once intonated (if there were kit strings supplied only use these for basic set up checking, fit some decent strings before intonating as those cheap strings are so inconsistent in sound and diameter along their length).

So if the saddles are too far back when you measure the scale length, then you quickly run out of movement for the bass strings.

And measure the scale length from the neck side of the G string nut slot to the mid-point of the G saddle, the point where the string will leave the saddle.

In the kit photo, the B,E and A string intonation screws are shorter D and G screws, just because their saddles will end up further back when intonated.

If you are going to use the pickups as humbuckers and aren't doing anything fancy with them like add series/parallel/split switches, then it doesn't matter which way round they go at all. The only time it will have any effect is if you fit a coil split switch, in which case the pickup orientation will determine whether the single coil is nearer the neck or the bridge. It's a small distance and won't make any real difference to the sound, but some people are fussy over these things. However, I have no idea quite how you'd tell except by empirical testing. There aren't any pole pieces to tap with a screwdriver to see which coil is working, and with that plastic cover, I don't know if tapping over where the pole pieces should be would give a clear enough sound to tell with accuracy.