Basically what I am trying to do is transpose every other column to a row with the following columns data beside it.
The source can have only two columns up to one-thou
If you are using SQL Server 2008, I think you should look into using the CROSS APPLY (VALUES) technique:
http://www.sqlservercentral.com/articles/CROSS+APPLY+VALUES+UNPIVOT/91234/
Basically, it goes like this:
SELECT
x.NewColumn1,
x.NewColumn2
FROM YourTable t
CROSS APPLY (
VALUES
(t.OldColumn1, t.OldColumn2),
(t.OldColumn3, t.OldColumn4),
...
) x (NewColumn1, NewColumn2);
Here's a runnable example: http://sqlfiddle.com/#!3/9a9d2/5/0