Here is the sequence for making the shaker:
1) Mount middle piece (part A) in Chuck #1, rough it to slightly oversize, drill it out, sand the open end FLAT with large sanding block. Leave part A in the chuck.
2) Mount bottom piece (part B) in Chuck #2, rough it to slightly oversize, drill the 3/32" through hole, shape the volcano and fit the joint to part A. Check the fit OFTEN as you remove tiny bits of material. Remove part B from Chuck #2.
3) Remount Chuck #1 with part A still attached. Glue part B into part A. Finish-turn the bottom of part B. Part off cylinder A near the chuck, making sure to get the top edge FLAT. Take a slow, fine cut and clean up on a flat surface with fine sandpaper.
** Alternate, single-chuck approach **
At the end of step 1, remove part A from the chuck.
In step 2, leave part B in the chuck, glue part A to it, and do a nicer job of finishing the upper edge of part A.
Reverse-chuck the A/B assembly into a jam chuck to finish the bottom of part B.
4) Chuck the lid piece (part C) last, rough it to slightly oversize, shape the inside of the lid ... and fit the completed A/B assembly to it. This is the configuration needed for the final "assembly sanding", to make sure the lid and body will fit together with no "stair step" at the joint.
5) Make a jam chuck to (tightly) fit the underside of part C, so you can finish-turn the top of the lid. My completed lid didn't want to come out of the jam chuck, so I had to carefully cut away most of the chuck around the joint.
I haven't applied any finish yet. Still thinking about it....
PS - If you don't mind filling the shaker through the bottom hole, go ahead and glue the lid on. Or, get fancy and make a threaded connection like Stu mentioned.