I've decided to buy some parts and put together a guitar. I was going to buy a charvel so-cal body, It is H-S-H configuration.

My silly question is, if I buy a pick guard with only one pick up in it, and the pick guard just covers the rest of the holes where the pick up's should be, will this have and problems?

Also, i haven't looked it up yet, but if i bought a fender neck with a nut, would that fit okay?

Thanks for your help guys!
The pick guard with only one pickup in will be fine.

Couldn't comment on the neck issue though. It will depend upon the neck pocket, the heel of the neck and whether they match up to give you the proper scale length.
Some Fender necks fit some Charvels. Others don't. Best you can do is measure everything very carefully. A better option would be to order a custom neck from a company like Musikraft, USACG or Warmoth (Musikraft would be my pick; USACG are a pain to order from and Warmoth don't roll their fretboard edges or the fret ends) and have them not drill any mounting holes. This way you can reshape the hele if need be and drill the holes yourself to make sure they all match. Bear in mind that most Charvels have an angled neck pocket.

As for the pickguard, it shouldn't cause any issues. By not having pickups where there are routings you may find the guitar becomes acoustically a little louder, but this shouldn't be an issue except when playing at very low volumes.
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thanks guys! i've contacted the seller about necks to see if he can give me an insite to what will fit.