I can see the thought process behind your workflow and in general, the concept is solid, but the techniques and tools used to create geometry are fraught with problems.
The key to good geometry, as others have mentioned already, is good curves. In Fusion 360 hat means sketches.
You re-meshed your triangulated scan data into a quad mesh.
Then that quad mesh was imported into Fusion 360 converted into a T-spline and then NURBS surface.
The NURBS surface was used to create an intersection sketch, to get a base profile.
One problem is that the dense mesh is full of poles (star points in T-Spline lingo ) which creates curvature problems, particularly when a sketch intersection is created at such a point.
For surfacing projects, I stay almost completely away from sketch projections of any sort and almost completely work with surface edges.
A better workflow and with a bit experience likely less a laborious one is to simply import the triangulated mesh and create a mesh section sketch.
That sketch you then use as a visual guideline only to start building a nice smooth curve.
Start with a 3-degree one and see if that works. Then maybe upgrade to a 5-degree curve.
Does not work either? Maybe use a fit point spline. Always toggle on the curvature comb display when creating such spline curves.
I recently helped another user in with another tail light and demonstrated the technique for him in a screencast: