How do I run a private pub server while still referencing packages from pub.dartlang.org?
You can set the environment variable PUB_HOSTED_URL so it points to your custom pub repo server. This way pub loads all packages which don't have a server specified from this server.
You can define exceptions in pubspec.yaml like
dependencies: transmogrify: hosted: name: transmogrify url: http://some-package-server.comsee https://www.dartlang.org/tools/pub/dependencies.html for more details.
There is another package that seems to provide a custom Pub repo https://pub.dartlang.org/packages/pub_proxy_server