I ended up figuring out a way to do what I needed with help from this post: How to include sources without PCH include - #5 by anonymous_user_d868c905
I have a file in my Source/MyPlugin/Private directory that I generate in MyPlugin.Build.cs, this adds #include "Foo.cpp" for the additional cpp files I need to include in the build. I also add the path to Foo.cpp etc into the PrivateIncludePaths in my Build.cs