Been down this road more times than I can count, so here's what finally made it click for me. First thing: don't try to model over the mesh directly. Import it, scale it to the right size using a known measurement, then just leave it sitting there as a reference while you build fresh geometry on top. Reverse engineering the whole surface feature by feature sounds noble but it eats your week.
The trick is breaking the part into simple chunks. A big round flange with bolt holes is just a sketch, a circle, and a pattern, no reason to fight the scan for that. Curved shells I rough in as a swept or lofted solid, then hold it up against the mesh and nudge until it lines up close enough. Close enough being the key phrase. If it's a cosmetic cover, nobody will ever notice a millimeter.
Holes and mounts are where people overthink it. Measure the real part with calipers if you have it, or check the mesh with a section cut. Standard drill sizes win every time over trusting a messy scan. Last tip: save your setup as a template. The second scan goes way faster than the first.