First and foremost, I'm not able to post photos of any of these parts. I'll do my best to keep things away from specific geometries. I just want to get a handle on workflow for this type of work.

I've got a handful of different .step files for thin fiberglass parts, some that have extrusions where they'll lay a core on the first component and then lay more fiberglass over the core (non-uniform thickness). Some will need to be split, some are fairly simple - like the shape of a luggage compartment cover on a typical commercial jet, but 0.035" thick. If it helps to imagine the geometries, they're mostly what you'd see as body panels on planes or radar equipment.

My job is to take the .step file and make a mold to make these. Customer requires a flange extending past the edge of the parts, and edge-of-part engravings, as well as holes drilled. 

My initial thought was to shut off holes and cutouts, create a plane where it makes sense for machining, then use Convert Entities on the outer perimeter of the part on the new plane then extrude up to body. I get errors saying that the body does not terminate the extrusion. I made the extrusion sketch larger, used a square instead of the geometry, smaller... No change. It eventually worked (no idea why) and I used surface modeling to create the flanges. I tried to project the perimeter geometry onto the surface of the mold to do a swept cut for the end of part lines, but that was hit or miss.

Mold tools seem very powerful, but I'm not sure that a single part tool for a thin sheet part makes the best use of them. If I'm wrong, some literature or videos showing me how to use them would be VERY valuable.

Does anyone else do this sort of work? What's your method, and can you help me resolve the issue I'm having with extrude up to body/surface giving me errors? I'm not much of a surfaces user, so I suspect at least some of my problems are coming from that gap in my knowledge. 

Thanks!