As already mentioned, any replacement pickups will need the pickup cavities modifying and a new scratchplate. You'd probably want to do that work before the guitar's all finished. The neck pickup rout will be covered up so is easy to do, but the bridge one is exposed and you will need to fill the cut-outs for the mounting lugs and re-cut them in the correct position, which will mean that you'll need to match any finish on the repaired area. So if you do plan to upgrade the pickups, it is probably best to do that from the start.