Project Guitar Help Centre: How To Mount a Guitar Neck
Bolt-on guitar necks are generally mounted to the body with four (sometimes six) screws and a rectangular metal neck plate to help evenly distribute the pressure and avoid the screw heads damaging the wood:

Fender's guitars are predominantly bolt-on (Stratocaster, Telecaster, Jazzmaster, Jaguar, etc) and fortunately, are very easy to replace - Leo Fender's intention when designing his first prototype guitars was even said to have been to create a guitar where parts could be easily removed and replaced as needed.
If you are starting with both an undrilled body and undrilled neck, you need to start by drilling the body.
Using your neck plate, position it in the correct place on the back of the neck and secure it down (either a clamp or a blob of blu-tak is fine - just as long as it doesn't move). There isn't any right or wrong answer when it comes to the placement of your neck plate - even two guitars made by Fender in the same factory in the same year will almost certainly have slightly differently-placed mounting holes for the neck.

It is best to position the neck plate approximately 3mm from the top edge and central to the neck pocket so that the spacing is roughly even.
With the neck plate in place mark the holes, then remove the neck plate again and drill:
Accuracy at this point is very important so it is best to begin to drill each hole and then use the neck plate again to ensure that the holes are lined up. You should also make absolutely sure that you are drilling directly down at a 90° angle - slightly wonky holes aren't the end of the world but they are best avoided if possible!
It is worth mentioning that at the joint between neck and body, the intention is for the screws to bite into the hard(er) wood of the neck itself rather than the body - creating a type of sandwich effect of the body between neckplate and neck, more evenly distributing the pressure and offering a more efficient transference of vibrations from neck to body (and visa versa).
So, the holes of the body can permissibly be slightly larger than the screw thread itself - this also allows a little bit of "wiggle room" if you're trying to align your undrilled body with an already-drilled neck.

With the body drilled, it's time to attach the body. The fit between neck and neck pocket should be snug but if you are struggling, do not force it too hard. Neck pocket widths are often shrunk by a matter of 1mm or 2mm because of build-up of the lacquer after the neck pocket is routed. In addition to this environmental factors such as heat and humidity can cause fluctuations in the wood (particularly in items with nitrocellulose finishes) which present themselves most prominently at the neck pocket areas.
For this reason it is always best to store both body and neck together in a room with stable heat and humidity (at room temperature) for a length of time (over night at a minimum) before attempting to mate them together. Inconsistencies between manufacturing and measuring for different parts can also play a key role in neck pocket inconsistencies, although we at KavanaghCustoms have done our best to always ensure our bodies and necks are built to exacting dimensions.
If you find that it is the case that the neck pocket is too snug, the two options are to either to resize the heel of the neck, or the neck pocket of the body, neither are difficult and remember that it will only ever be a matter of millimetres so take it slowly.
For the body, use a piece of high-grit sand paper and gently widen the neck pocket slightly on either side to accommodate the neck. This can be a slightly arduous task but take it slowly (or risk chipping a piece of the lacquer off from the neck pocket edge) and check back with the neck frequently to make sure you don't widen it too much.

The same approach should be used if you instead chose to amend the width of the neck's heel. Amending the heel may prove to be a less difficult task as there is only a tiny area on either side of the neck that needs attention. Using a high-grit sandpaper will ensure that the resulting area doesn't bear any marks.
Do not be tempted to use power tools for this task. Although the attraction is there to speed things up, you run the risk of knocking pieces of the lacquer off around the neck pocket and it also greatly increases the risk of you widening the pocket too much.
Once the body is drilled it is time to mount the neck. It is best to use a vice or clamp to hold the neck whilst you get it exactly into place and then, using a drill bit or other sharp object, mark the neck through the freshly-drilled holes in your body, in the same way we marked the body using the neck plate for guidance.

Once you have the neck correctly marked, remove the body again and carefully drill into the neck, ensuring as before that your direction is 90° to the neck. You must also ensure that you do not drill too deeply or you run the risk of coming back out the other side through the fingerboard.

At this point some guitar technicians decide to use a low-grit sandpaper to remove the slick surface finish from the rear of the neck where it comes into direct contact with the body. It is believed that roughening this area helps with transferring vibrations from neck to body and gives a more snug fit. This step isn't essential in your guitar build but is worth mentioning.
If you are at all concerned about ensuring that your neck is mounted perfectly straight within your body, thread a string through either side of the bridge (both high and low-E) and run them right the way up the neck and into the machineheads. With the neck seated into the pocket, tighten the strings until they become slightly taught and then check the line of the strings against each edge of the fingerboard to make sure they don't "fall off" either side at the bottom end.
One you've done this, and both the neck and body have been successfully drilled, use the screws to 'bolt' the two together. If you have trouble threading the screw and meet with a lot of resistance, try rubbing soap into the threads to ease it in:
You should tighten the screws in phases - tightening each one a (small) set number of turns each time, and checking to make sure that the neck is still straight (using the two strings you strung into it at the last step), until all four are tightened. Don't try and tighten each screw all the way in turn - it gives you less opportunity for adjustments and can lead to inconsistent spacing between body and neck.
Once that's all done, you should be set to finish off the rest of your guitar or just string it up and play.
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