Data Layout Conversion (Advanced Rows to Column ?)

Hi,

I have a large CSV (comma delimited) which has data laid out in rows and each row contains about 10,000 separate inputs. This data is an output from a Simulink Simulation where variables have been saved on to the workspace saved as a .mat file then converted into csv (using a tool my colleague wrote). This tool was a modification from a script provided by mathworks therefore quite complex to modify to save the data in the format I need.

Ive attached a spreadsheet with this post which contains the format the data currently is (input) and the format I need it to be in (output). As its an output from simulink some data are multidimensional arrays therefore not all the data can be converted straight from rows to columns. I have used the "Paste Special" and transposed the data for now, but I will need to do this repeatedly therefore looking for a better solution i.e. a vbscript that can do this for me.

Any advice/solution would be appreciated.

Thanks.

Edit: Forgot to mention, the data might always not be in the same format. For e.g. sometimes the data might just be in the following format without any multidimensional arrays..
Header 1
1,2,3,4,5...
Header 2
3,4,5,6,7..
Header 3.. and so on.