Having struggled with this for what seems like an eternity - and has since resulted in the project being put back by some considerable margin - it was reading through some more blogs that I came across what seemed to be the solution to the Masterpage problem (see previous posts).
By developing a feature that will create a site based upon a specific Masterpage and have it deploy correctly, the feature creation was OK and seemed to work but the associated contentTypes I could get to be created at the same time. After a lot of time yesterday the feature installed, but only at a site level because if the scope is changed to 'Farm' or 'Web' it would not install. So with this in mind I copied the relevant files to the WFE and installed/activated the feature. Created a new site on the backend as it was created as required and then ran the deployment - guess what the Masterpage was reset again!!!!
This has gone beyond a joke and I would recommend anyone thinking about going down the customization and deployment routes to seriously consider the time and resources required.
We will be raising this issue with our Gold Supplier and get them to raise a ticket with MS.