I am so glad I found this game again! its so awesome especially now in Open Source

I do however need help, to figure out how to sort the trains signals, I've read all the Wiki pages regarding Signals and the various tips, and I am using a lot of signals (although it is confusing so many different types - I think I have combination of various one way and both way signals..).
I made many merges, parallel tracks, all the tricks I figured out, and still my trains managed to create a traffic jam and forcing me to constantly oversee that single project I have.
Screenshots are attached, please help me figure out what I do wrong, and how to make it better, I am out of ideas for that area...
Thanks!