well, it will not hurt to do that. if you plan to store it while waiting on the topend to be done, just pour some 2 smoke oil on the bearings if ya can. then cover the bottom end with something to keep dirt and moisture out.
Great you are on the right track. Get back to us when you are ready to start it for info on how to break it in and the tests you should make prior to starting.
A good move is to browse the forum and search for "leak down test" as you should do one prior to starting!
Don't be scared to put a fair amount of 2 stroke oil on the piston and rings when you assemble them. Make sure that the gaskets are not those green or blue paper things, get OEM or Cometic gaskets. Use a new head gasket and tension them down correctly.
There is a free downloadable manual on the forum somewhere.
Have a look at this video to get a better idea of how two strokes work, aptly, the video is narrated by an Australian, so Blaaster, this one is for you