I have the same kit and I am just waiting for the weather to get warmer so I can finish spraying it black and hopefully I can get to the shop to get some paint and wont be in lock down like the last time I wanted some paint.
If your tuners are the same as mine you can mount them either way as the design allows for the different direction in load. Slop between the gear and threaded spindle it will always be zero as the load is always in the one direction as when you tune the guitar it is always increasing the note due to putting tension on the string. This loads one face of the thread and the gear and if you were to reverse the orientation of the tuner then the load will be on the opposite face of both items but the slop would still be zero. The gear and spindle are not of a quality that you experience full face contact on both parts so there will be one side that has contact and the trailing side will have fresh air between to two mating parts. If you reverse the tuners then the load on the threaded spindle will be in the opposite direction and that is where you would have to look at the design and whether you can reverse them but on the ones supplied with my kit the load on the threaded spindle is easily overcome due to the way the spindle is mounted in the base and the way the spindle is cast. To align the tuners I put a straight edge across 2 opposite tuners so they are parallel to each other and perpendicular to the neck centre line.
The only reason you have to mount the tuners as Simon has said is due to the position of the holes drilled in the head. They are drilled lower towards the nut when held in the vertical position and if you were to reverse them then they would not look symmetrical so the button has to be above the spindle so they look central to the head.
As for the position of the pickups the factory really has to move the pocket towards the bridge as I find it to be a real pain on all 3 models I have bought. I was going to slide the neck out to allow for the ring but then I was having a problem with the bridge position and not having enough adjustment to allow intonation. When I was looking at sliding the bridge out I was going to put a packer between the neck and body to make sure the position was correct and to give as much contact between the neck and body as possible. My solution was a little different as I already have a Precision and Jazz bass and wanted a bass with a different pickup, so I bought a copy of a Music Man bass pickup that will be positioned at the bridge position and I am making a full face pickguard that will cover up the pickup cavity near the neck.
As mentioned in other build diaries some people have experienced problems with the bridge mounting plugs pulling out of the body due to how tight they are in the wood and the tension that is applied by the strings. I was going to solve this problem by buying some threaded inserts that screw into the body. I was going to make some out of a stainless steel bolt but found it cheaper to buy some from Amazon but of course the ones I wanted are no longer available but I am sure I will find some similar when I really need them and if not I will just make some out of a bolt.