Stephen, surprised there haven’t been any replies on this one.
I don’t know what tools you have access to, so I’ll go through a general milling for you. First, you always want to cut oversized when milling. I would rip the boards to at least 3 1/4” width, maybe 3 1/2”. If you have one flat edge, you can go right to the table saw to rip, if not, you need to make one edge reasonably flat. A few quick passes on a jointer will do this, or there are jigs and methods to do this on a tablesaw.
Next, take you 4 blanks to the jointer and make one face flat. Watch grain direction to minimize tearout.
Next, take 4 blanks with flat reference face to the thickness planer. Plane with reference face on the bed until you get the top flattened (the planer is cutting the entire top face of the board). Take shallow cuts, watch grain direction to minimize tearout. Once you’ve got both faces flat and parallel, if you’ve still got material to remove, flip the board and alternate taking some off of each side. It’s best to do all 4 boards at the same time so they are the same thickness when you are done (final pass on all 4 boards is done with the same setting on the planer.)
If you’re removing 1/2”, you might want to mill close to your final thickness and stop, leaving some meat to be removed. After a few days the wood may move and this will give you some material to play with to get it flat again.
Once your done at the planer you have 4 boards of the same thickness that each have two flat and parallel faces.
Now, back to the jointer to joint one edge. Watch you feed direction to minimize tearout and joint one edge, doesn’t matter which.
Next, back to the tablesaw. Rip the edge that is not jointed. Now you can rip to final width. (If you’re going let the wood sit to see if it moves on you, don’t rip all the way to final width yet, leave some fat) When you rip to width, rip matching pieces at the same time, with the same TS setting, so if they are off a tad, at least they are identical. In your case, rip all 4 pieces without moving the TS fence.
Now your boards are flat and square on 4 sides.
Lastly, crosscut to length.
For you shelf, you can use the offcuts from ripping the rough boards to width, mill them, and glue them up to make a larger board. I would NOT try to squeeze three 3” wide blanks from a 9” board (which, when you subtract the saw kerf isn’t actually possible anyway) you need to leave yourself room to remove material in milling.
Hopefully this helps,and addresses your question. Let me know if you have more specific question.
-- John