Hi Dave,
I opened a new thread for this topic because these build and bug discussions don’t fit into here: Prototype for the new MI Plaits in VCV Rack
I am going to post updates in the other thread, feel free to ask your questions in there as well. Looking into your error message I assume that your Makefile does not include all the new directories. Simply have a look at https://github.com/tobiza/AudibleInstruments/blob/master/Makefile and compare it with your version. The SixOpEngine is part of “SOURCES += $(wildcard eurorack/plaits/dsp/engine2/*.cc)” for example.
Greetings, Tobi