The "Waiting for Clearance" message is a bit confusing, however. I've noticed that the AI will say that when they pass trackmarks, or stop at certain passenger-enabled stations. This is confusing because I don't know what they're waiting for, and I've wandered off to hunt down Alister, or Moira (the female Alister) who also causes a few problems, only to find there wasn't any issue in the first place.
One of the things that I do, that seems to help most of the time, is to place periodic signals even in the middle of double-track sections. I use the US-Coal 3000T consist as my ruler, and place signals every consist-length plus a little smidge. I find that after doing this, I can keep the AI moving along pretty well without snarling junctions most of the time because this spaces out the AI and slows them down enough so that one train will run on the "yellows" behind another.
I too have reworked junctions, stations, and whole sections not because they didn't look right, but only because the AI didn't like them! In my more recent case, I completely renovated my Eastport passenger terminal by moving it nearly a mile or so into the city. This gave me longer leads into the station, and therefore more time for the AI to sort things out before they ganged up on the junctions.
One of the things I noticed recently, is that the AI will become brain-farty when the system memory gets low. After being in Surveyor for nearly 5 hours, then in Driver for nearly 3, the AI drivers will start to randomly take the wrong paths when they reach junctions that they otherwise didn't have problems at a previous time.
John