Basically, a few days ago after starting the 'Battle of Whiterun' quest my game started to CTD when saveing (auto, quick and via menu) and when entering dungeons (before loading screen finishes). These issues only start to occur after travelling to a new area (even within the same cell) and after having waited for 24 hours (in-game of course). Any and all help is greatly appreciated.

If your Autosave got corrupted, and then you loaded it and even created a new save slot, your save is still corrupted.

Do you have a save slot from before this happened?

Unfortunately not for this particular character, I'd already overwritten my uncorrupted saves before I'd realised the extent of the problem. Am I totally screwed?

You can try deleting the tmp.ess file in Windows Explorer, but that may not get rid of the root issue that cause the corruption.

BTW, if you were adding and removing mods from your save, that is the most common reason for corruption. And, this corruption does not always appear until days or weeks down the road. If you think this was the reason, then make sure you always create a forked save before adding any new mod to the game. (you can add the mod, load your save, then make a new slot, no need to make the forked save before you install the mod) This way you can remove the mod, and load the save from before you activated it and play on from there.

I had this issue recently with one character and had to start over completely because all of my saves for that character ended up with the same temporary save issue. My problem was mod related, so have you installed any new mods recently?

Not recently no, but the problems started occuring during the battle of Whiterun (imperial scenario).