Hi there. An excellent effort to attempt this.
My position at the moment is that I don't intend to update this project to FFGL 1.6, so if you succeed that will be a very good thing I am sure. I looked into FFGL 1.6 for 64bit but came across some peculiar problems and have not had time to continue with it. I am not using the Resolume FFGL source, however.
One thing to note is that ShaderToy has changed iGobalTime to iTime and added iDeltaTime, iFrame, iFrameRate and iSampleRate, so recent shaders using these will not work with the existing code.
I might update the ShaderMaker project for these uniforms because it is already 1.6. In fact you might get answers to many of your questions by looking at the ShaderMaker code.
I have recently updated ShaderToySender for the new uniforms. This is a stand-alone program equivalent to ShaderLoader, which produces a Spout output and is available to Spout supporters. There are some advantages over a Freeframe plugin such as loading the four textures and other things you can do in a stand-alone program but not in a plugin. If it does what you want, it might save some time. More than 200 shaders are included, checked, tweaked and working.
In fact the ShaderLoader plugin is stretching the boundaries of what Freeframe is designed for and it is really only by by good fortune that it does work.
If you want to remove the SpoutPanel user interface, you will not be able to replace it with any sort of dialog or it will freeze the Resolume GUI. That is the reason for the complicated process in the first place. You may be best to stick with a simple copy/paste of a shader file path. At least that will be remembered in a composition and you will not need a registry entry to save the shader path and recall it. Then changes happen when Resolume expects them to. Maybe you could try that to find out whether it solves your current problem.
I hope that you succeed in the project. I can only be of limited help because I am not using FFGL 1.6 and I have come across some strange problems as I said before.
My feeling is that a dedicated shader module for Resolume is the way to go, maybe ISF instead of ShaderToy.