A couple thoughts:
For alignment, just use holes. There are a number of ways to do this, depending on what you are trying to align, the most obvious is for vertical alignment of layers, where the holes would be dowel holes. Horizontal alignment doesn’t seem to make this feasible, since the machine won’t cut into the side of the material, but if you cut a half-cylinder in the top surface, you can get alignment using a cylindrical or half cylindrical key.
I would section this as layers and cut the layers as lamina (vertical edges), then do final shaping by hand, unless you have a real interest in getting into some of the more involved features of Fusion or Inventor or Solidworks. There are awesome videos for using the shaping tools in Fusion and Inventor on the autodesk website, but they can be a bit hard to find and the tools are not simple, no matter how it appears in the videos.
To do it in one shot in inventor (and, I think, Fusion), I might start by making a helical curve on a cylinder and using that as a guide for a loft sweep. Then I would start using the surface modifying tools.
If you are going to do this as a mold, as others have suggested, and I would also suggest, then using foam and hand shaping and finishing is a rea good way to go. For foam, I like surforms and microplanes. Surforms (Stanley made them, as do others) are the hand plane/rasp hybrid that takes replaceable blades. They were originally designed for use on foam when making surfboards. Microplanes are minature versions, and are awesome for detail work, and come in shapes that let you do inside faired surfaces. I think they actually started as a hoopty do kitchen tool, but they were adopted by woodworkers and modelmakers. After getting the form you want, a thin layer of mold surfacing material (I am not a pro, so I have used a number of things, including both cheap polyesther resin and epoxy) that can be smoothed and polished so you transfer a good finish to the final product. Planning it as a mold may make cutting it a lot easier, since you will be less concerned with perfect out of the machine, and you will have predominantly external curved surfaces o prepare, rather than internal.