Hi and welcome.

There does seem to be a small mismatch in the TL kit as the scratchplate is drilled for height adjustment machine screws, but overly-short woodscrews seem to have been supplied. Maybe it's something Adam needs to look into.

Your pickguard was designed to be located so that it butts-up to the end of the neck. But maybe the position of the neck pickup slot prevented this? Have you got any pictures of the build prior to this, or can you give us some shots of the whole body from the top, with and without the pickguard fitted? If the small semi-circular cut-out in the pickguard is also butted up to, or very close to the metal control plate at the moment, then it may be that there is an issue with the neck pocket routing.

From the photo, can we assume that this is a left-handed kit, or is it just a flipped photo?

With regards to the pickup, the neck pickup in a Tele is often positioned quite low, but you should be able to raise it a bit higher than that for a stronger output and tone.

I'm not familiar with that particular kit, though I have several Teles, but I would either expect there to be some foam stuck under the pickup (to allow for body mounting), or maybe some springs or rubber tube, so that there was something keeping the pickup pressed upwards against the screws, or else some machine screws and springs/rubber tube supplied so that you can mount the pickup from the scratchplate and use the machine screws for height adjustment.

So, is there any foam rubber/springs/tube located under the pickup, or is it held purely in place by the screws being wound through the pickup's plastic baseplate? I'm just wondering if there isn;t anything underneath it at the moment, then it may sit higher if there is.

Otherwise its either a) source some longer thin wood screws and maybe add some foam or springs underneath it, or b) source some pickup mounting machine screws and springs and mount the pickup from the pickguard. An eBay search for 'Fender pickup mounting screws" (and/or springs) should turn up plenty of sources.

Or you could simply cut a piece of plywood to fit the bottom of the pickup slot (doesn't have to be perfect), stick it in and screw into that.

But I would like to know what the whole body looks like. I don't recall any major issues with the RH Tele kit, but if this is a leftie, then there may be some factory issues that Adam needs to sort out.