@Lindon Yes you spotted both of the main issues:
JuceHeader collision. Previous versions used #include "../Binaries/JuceLibraryCode/JuceHeader.h" which was fine for the DLL, but exporting to VST3/AU caused the JuceHeaders (project info like companyName, versionString, etc.) to be pulled in twice. Solution is just to use #include <JuceHeader>
.cpp.inc is resolved on all Fx to just .cpp (it was a leftover from the batch compile I ran).
A handful of effects couldn't be compiled together — some of the amp/saturation nodes (the ones based on a shared __Gain_H template) and a few of the k-reverbs. Individually they were fine, but combining them caused build errors. It came down to a couple of effects accidentally reusing the same internal names behind the scenes, so they stepped on each other once everything compiled together. That's now sorted out, and the full set compiles as one.
The repo is up-to-date now and should be more stable.