Hello there,
A Fender Standard Telecaster neck will fit in the neck pocket of a Squier Affinity Telecaster body. The heel width should be the same. The shape of the heel shoulders are the same. The heel thickness may not be identical (discussed in action discussion below). The Affinity has been made in a few different locations and the specs are not exactly identical. So, you may have no problem or there may be some fitting required.
Most likely issue you will face is getting the string height (action) playable. This may require a shim.
Another issue that may arise is intonation (ability to play in tune all the way down the neck). The Fender Standard and the Squier Affinity Teles both have a 25 1/2 inch scale length. However, the mounting holes make not be in the same location. The neck will bolt on fine. But after it is on, you may not be able to set the intonation. The cause of that is the mounting holes were drilled in different locations. To fix this, you plug the holes on the neck and drill new ones at the proper location for that body.
As for pickups, please remember that the Tele body is routed for a specific pickup configuration. So swapping a single coil for a humbucker (for example) requires altering the pickup cavity and replacing either the pickguard or the bridge (depending on location). Also the Tele neck single coil pickup is not the same exact specs as a Stratocaster pickup. The Tele bridge single coil has a different mounting. So Stratocaster pickups are not a simple drop in on a Telecaster.
If you swap out the pickups, do swap out the pots. Fender uses a much better grade of pot than what is in the Squier.
Frankly, I think this is a waste of money (unless you have the parts on hand). The cost of better pickups, better pots and a Fender neck is about what the Squier cost (more than it is worth now). With the upgrades, you will not get your money out when you sell. You will need to part it out to get part of your money back when you sell. Also, if you sell the Squier and with the money you would spend on parts, you can buy a used Fender Standard Telecaster. If you do that, you have a much better guitar.
Later,
Norm