Here’s two ways that I know of to add project dependencies.
void addProjectDeps(Project project, Configuration config) {
Project p1 = project.project(':project1');
Project p2 = project.project(':project2');
DependencyHandler dh = project.getDependencies();
dh.add(config.getName(), p1); // only works when project.configurations.contains(config)
Dependency d2 = dh.create(p2);
config.getDependencies().add(p2);
}