Dale,
I cut my joints almost through on the tablesaw while the blank is still rectangular. I leave 1/8" to hold the bait together for shaping.
Once the profile is cut out on the bandsaw, I drill my ballast holes on the drill press, so I can keep the blank square and keep the holes centered. I also drill a small through hole at my eye location so the eyes will line up later.
I do all of my rough shaping on an oscillating belt sander.
I add detail with a dremel and it's sanding drum, and an exacto knife.
Then I cut the joints completely through with a drywall knife after my shaping is done.
I clean up the pieces on the belt sander, and do the final joint shaping.
I install my screw eye hinge parts, mark where I want the slots on the next section, and cut/shape the hinge slots in the front of the next section.
I have a drill press table with a small centering pin that lines up with the center of the bit. I mark where I want my hinge pins to go, use an awl to mark the holes, and then put the right size bit in the drill press. I put one side of the piece down so the awl hole is on the centering pin. I drill half way down from one side, then flip the piece, put the starter hole onto the centering pin, and drill down to finish the pin hole.
If I do it right, the two holes meet at the center. If not, because I have the hinge slots already cut, I can see where the holes miss each other, and can use a hand held drill to correct the alignment. It's not hard to do.
Having a process has made it easy for me to make a new jointed bait, or multiple baits, if I want to.
I hope this helps.