I thought I'd randomly choose an issue and take a crack at it.
I've started trying to understand Gradle's internals but it's slow progress. As I think I understand things, I have tried to add some JavaDoc cough, cough along the way if I'm resonably confident it's accurate....

I've never tried to debug such a complex / large Groovy/Java project, and the Groovy code by it's dynamic nature is much harder to debug.

Is there any internal architecture documentation anywhere by any chance?

From what I can tell so far, I need to add a ExcludeRule to the Ivy system. I am trying to track down the point of interface between Gradle and Ivy but it's proving to be a little elusive. I've found:

new DefaultArtifact(moduleRevisionId, null, baseName, groups.extension, groups.extension, extraAttributes)

but I haven't figured out yet why you don't hold onto a reference of it.
Care to point me in the right direction?

I've attached the stuff I've done so far, as well as doing a little refactoring in Main.main.

I'm pretty keen to nail this, so I will keep working on it...

You have chosen one of the hardest parts to get into. Ivy is pretty complex and we have a layer on top of this. Without waning to spoil your fun in getting into this The ModuleDescriptorConverter is the place to have a look at. It corresponds to an ivy file (ivy.xml). The global excludes apply to all dependencies.

The global exclude statement would be a top level dependencies directive:

dependencies {
   exclude ...
}

In the ModuleDescriptorConverter you can call from the created Ivy moduleDescriptor the method addExcludeRule. Have a look at the ModuleDependency where we offer excludes for a single dependency.