Online on another 2j I saw a tube going from circle to circle and was wondering what it's normally used for and if It's supposed to be missing on my car.The higher up circle is capped. (2003 Lexus is300 stock)

 

It is supposed to be missing on IS300s. On other cars, there is an air-assist power steering valve, But they replaced it with an electronic sensor on IS300s. The hard pipe you don't have to worry about, but that rubber plug on the intake manifold.... keep an eye on it. They tend to degrade and crack with age and that will cause a vacuum leak. If you ever get surging idle, check that cap