I have basically made my Skyrim save unplayable, I had downloaded the Civil War Overhaul and done the first set up quests up until the defence of Whiterun. I did some thing that broke the quest chain and finally installed the mod and carried on with the standard civil war until I realized I was being instantly attacked in every Stormcloak city. I've attempted to yield, pay the bounty in console, set my overall bounty to 0 but absolutely nothing works. Does anybody have any idea on how to fix this problem with a mod/command?
There are two important points you missed, both contained within Civil War Overhaul description. Since mods creator, Apollo Down, is a masterfull wordsmith let me just quote the relevant bits from the Nexus page.
One - installing CWO during the gameplay:
YOU MUST START A NEW GAME. THERE IS NO WAY AROUND THIS. AT ALL. SO DON'T ASK ME. BECAUSE YOU MUST START A NEW GAME. YOU MUST START A NEW GAME. NO, NOT AFTER YOU EXIT HELGEN THE FIRST TIME, NOT BEFORE YOU START THE CIVIL WAR, NOT AFTER BREAKFAST,YOU MUST USE THIS ON A NEW GAME WHERE YOU CLICK ON THE TEXT IN THE MAIN MENU THAT SAYS 'NEW GAME'. YOU MUST START A NEW GAME.
Without following a requirement that clear you can't really expect help with any problems you encounter.
That said, point two - Stormcloaks attacking you.
Basically, after the first siege of Whiterun, the guards in holds your faction does not own will be hostile toward you. All enemy soldiers will be hostile to you as well. Let me say this again because I get a lot of questions about this: HALF OF SKYRIM WILL BE HOSTILE TO YOU. THIS INCLUDES CITY GUARDS IN HOLDS YOU DO NOT OWN. THE ONLY WAY TO STOP THEM FROM BEING HOSTILE IS TO DISGUISE YOURSELF IN THE OTHER SIDE'S ARMOR, OR TO TAKE THE HOLD FOR YOURSELF.
What you see is not a bug. It's a feature introduced by the mod you just installed. One of the first features it advertises. So either you wear a disguise or uninstall that mod and hope that this script does not stay active.
Also, reading mods descriptions will go a long way for a healthy Skyrim modding experience.