It appears that Pepkura's output will require a huge chunk of work to clean up to get to the ultra-crisp and refined Prototyp model standard. This work will be a bit tedious with all the layered 1pt fold lines and separate outline objects that Pepa likes to place on the shapes. That said, I think this approach is far better than doing the work all by hand with 2d drawings!
One hard lesson I've learned is that while organizing Meta model components in separate layers makes sense to keep working around in the CAD model from becoming unweildy, it prevents Pepa from automatically generating tabs to connect those parts together. So there needs to be an intermediary step between the "live" CAD source and a "baked" model for Pepa to process... What I discovered in dealing with all this was Pepakura's handy 'reload model' workflow. I can build up changes and tweeks in CAD, reload the model in Pepa, and have those new bits add themselves to the existing ones.
The LMR's CAD source model and the part splits and tab assignments in Pepakura have stabilized, so it's time to bash things together and see how the design shakes out. Parts get pulled from Pep's manic eps output files into test-sheets and given a thorough clean-up of linework, fills, tabs, and then organized into reasonable arrangement. Print, cut, build.