Gear oil and engine oil should be drained when the components have been warmed up, preferably by a ride when possible. Gear oil comes in various colors but all of them darken with age. You drained the old oil. Forget about its odor and how it looked if it didn't have chunks of metal in it. You replaced it with a specified grade. If you used the specified volume, you're good to go.
The transmission has a small vent as pictured below. In 100,000 miles I haven't felt the need to investigate it because no leaks caused by excessive pressure have been evident. I replace gear oil at the beginning of each riding season.
