When you tell us to make sure to set the traffic lights correctly, what does that entail? Is it a guess and check process, or can it be determined without guessing?
Most of the time it can be determined without guessing, in the menu you can see the numbers and their corresponding sides (e.g. 1 = main, 2 = side, etc.) but sometimes it is not very clear what number belongs to what traffic so then it's just trial and error.
In the traffic rules tab select the speed limit and enter the desired speed limit in the textbox. Then click the traffic helpers (the white lines with car written on them) to set their speed limit. To remove the limit (default is 50) hold shift and click.