For anybody needing help with this, my problem appeared to be that Magento drag and drop didn't like when I moved a new Level 1 category between two existing Level 1 categories, to achieve the desired navigation the path I took is below.
1) Empty the categories you want to move of all products.
2) Create a new main level category but do not position.
3) Move all empty sub categories under the newly created main category.
4) Re-populate empty categories with original product data.
5) Access you sites database and open table catalog_category_entity
Within that table you can see all categories. The fields we are interested in are position and path.
So a single value within path such a "1" denotes the root magento category.
Two values separated by a "/" such as "1/2" in this instance refers to magentos "Default Category".
I place all my required categories as sub-categories of the default category. So my Level 1 categories will appear with the path "x/x/x".
For example 1/2/4, where
1 = magento root category
2 = magento default category
4 = ID of my Level 1 category
So if I want to reposition Level 1 categories without using the magento drag and drop I can change the position field values (Column to the right of path in database) for my level 1 categories.
For example:
path position
1/2/4 1
1/2/5 5
1/2/6 2
1/2/7 4
1/2/8 3
I know this appears quite complex, if anybody has any problems or questions please ask away.
Also i'd like to note that I do not recommend you alter database values directly unless you know what your doing and is a last resort. This solution only came about after 3 database rollbacks whilst trying to find a solution within magento.
Thanks