Fusion
It has to do with combination of settings, you need to select geometry you intend to cut then restrict tool from going into places that you don't want to cut. I made patches to cover pockets adjusted stock in setup and few other details, take a closer look all around.
T1 was crashing because flute length was smaller then depth of cut, I am not sure why you have it set as having 2 flutes, seems odd to me but I left that alone.
Which T1 are you refering to when you say it was crashing?
It is set to 2 flutes because it has 2 flutes. All the tools I am using here have 2 flutes. It is a router, not a mill.
I see in the rough 3d pass you have selected the top of the bottom radius as the machining boundary. If we cut that boundary first with the outer coutour pass why do we need to go down there with the rough 3d pass?
This brings up another question. Why can't I select the bottom edge of the upper radius? When trying to I get all these wierd selections.
Can you explain all those bodies you added and how that makes the finish tool path end at the bottom of the upper radius? My finish tool path goes all the way to the bottom of where the rough tool path went some, but not all the time. See below picture.
Contour using T1 had 1." flute length, it crashes in simulation because shaft rubs against model as tool gets deeper than flute length, oddly enough it seems to stop only if using holder while using shaft results in sporadic red flashes but keeps running.
For Parallel, I selected Silhouette in geometry tab than set bottom height in heights tab to bottom of top radius.
Patches are there to prevent tool from going into pockets in Parallel tool path, they are selected in addition to setup model for that operation only.
I used patches on holes and pockets, for the front neck area, I created surface offset with zero offset value then moved it to line up with top surface.
I set top height above top surface to include it into the tool path, if set on model top, tool does not finish that surface, neither does any other tool because you set that as top of your stock.
If I was making a guitar, I wouldn't want raw stock to be top surface, I would want to machine all surfaces to uniform texture.
Selecting "Contact Point Boundary" is key to completing bottom edge of top readius.
Selecting "Contact Only" didn't work to avoid pockets and holes, so I used patches.
If you have problem selecting bottom edge of top radius you can offset plane then project top surface onto it and delete all edges except perimeter, then select that as your cut outline for parallel tool path,..... or use another method as I did.
I don't work with wood, that's why 2 flutes end mills are odd to me, but figured there must be a reason for it so I left that alone.