dont screw it in yet, move the jack into a position where the gaps are not seen and pencil mark the holes. Not sure about the bridge on this model i think as to position to the neck its a pocket pickup so by rights the bridge pocket should be in the correct position. Use a long straight edge to find the center of the neck and measure the scale. There are videos in the "help section? I would advise to review everything before screwing or setting anything.
You need to know what you are trying to achieve, and then work out how to achieve that.
What you want is for a) the neck to line up with the body so that the strings run down the neck parallel to the edges (not to each other as the string spacing is wider at the bridge than at the nut) and the strings run over the pickup pole-pieces as centrally as possible and b) the bridge is located at the right distance from the nut so that the stings can be correctly intonated within the range of the saddle adjustment.
The neck/body join shouldn't allow much room for movement. Some movement at the moment is good, as you'll be applying finish to the neck, which will make it a bit wider and deeper, so it will then fit more snugly. In general I'd be looking for the beck to fit tightly against the longer edge of the pocket (the low E string/thickest string side) and be firmly up against the body end of the pocket.
Whilst it would be nice to just use the dot markers to indicate the centreline of the neck, on the kits these can be offset a bit, so it's best to use string as Drashkum has indicated, to check for correct neck alignment.
The rout for the trem block doesn't allow for a lot of positioning choice when positioning the bridge. The trem block will normally sit pretty much centrally in the hole, but a bit closer to the front edge to the rear. Whilst you can set the trem up for both upwards and downwards bending; downwards is the main use, so you need sufficient space between the bottom edge of the block and the rear of the trem rout to allow the trem block to move backwards as you push the trem arm down. Too close to the rear and the trem block can be physically stopped from moving before you've got enough drop off in pitch from the strings.
The scratchplate has some positioning movement available at the trem end, but it should fit snugly round the neck at the neck end, so its position is pretty much fixed there.
So you've got some slight movement available at the bridge end to move things so the stings line up correctly, but not a lot.
It helps to look at pictures of the real thing to get a good idea of how the relative positions of items should generally look.
Note how the trem plate sits in the cutout of the trem plate. Pretty well in, with a small even gap all the way around. Note how the high E (thinnest string) saddle is pretty far forward on it's adjustment screw. That's the sort of position you want the high E saddle to be when checking the scale length.
Have you read through the main Pit Bull build guide. It's still not fully comprehensive, and don't set the saddles mid-way when setting bridge position, set them almost as far forward as they will go, but it's better than the quick guide that came with the kit.
For the moment, I’d use cotton or very thin strings (not guitar strings) and just tie knots. You don’t need to fit the tuners for this if you want to, just run the string down the first tuner hole, back out the last one and then back over the nut and back down to the bridge.