When I delete C and then install windows fresh, is there any danger of me formatting over the other partitions by mistake, as I can't afford for that to happen.
Of course there is a chance that you format other partitions by mistake if you use the installer program incorrectly. The Windows installer is by default greedy, and you will have to tell it exactly what you want.
I have replaced a C partition (while also having D,E F etc.) countless times without any drive mapping problems. After all, if you have no other operating system, and delete/format partition C, and Windows is (was) on C, what is going to remap the other partitions ?
Just backup your existing C drive. If you feel shaky, backup the lot.
Reboot to a standalone partition manager.
Have a good look.
Delete the C partition.
Reboot to the Windows installer CD.
And tell it to install Windows in the empty partition.
In this way you get around problems that the Windows installer refuses to install on an existing partition with a Windows operation system on it, or gives you a hard time if you try.
Note that if you have programs installed on partitions other than C, they (mostly) will have to be installed again as the registry no longer knows they are there. Your Application Data stuff will be gone too.