Layout

I had this same issue at one time and the only thing I found to work was to demolish a few buildings to cut down on the population. It seems that when you have more than 3 large buildings along one street it causes traffic issues. You can always replace the buildings and hold out upgrading them until you have enough resources.

If it's a specific building that you just upgraded, you can temporarily move the buildings next to it to another spot, make an intersection on either side of the upgraded building by adding roads where the buildings were that you just moved, upgrade the small section of road, demo the temporarily added roads, and place the neighboring buildings back where they were.

(I've not done this myself but I noticed that residential buildings only care about the 2 squares of road they're touching)

I had the same problem. Took a lot of time to bring it back to 100% happiness. I wish EA would update the game with a tool for changing layout, a preview of the layout made with stat changes and other stuff to consider in rebuilding/changing your city and placement changes. Also, a "continue later" tool to save existing layout plans. rearraging is such a pain without a tool to use.