The client cannot get the Payment Pro account, but originally this was going to be the case and I ran the checkout wizard based on this, selecting the Payment pro option from the wizard. After the client changed their mind I re-ran wizard again but using the standard option. I think the fact that you say yourself the term standard is confusing is more confused by the fact that in your wizard you only offer 2 options standard and pro. So in previous outline I am referring to the fact that I selected the standard option in the wizard.
I have noticed when looking at the script that is produced it has duplicated code where the wizard has been re-run. Also despite changing to the standard option I find the Paypal account password in the script. I believe it should only include this if the pro option is being used. So in this respect re-running the wizard is not overwriting/replacing script it is adding to it! I have also tried as per your suggestion changing the names of the files the wizard creates (on the last page of the wizard). As I stated in previous post it comes up with an error saying a file is missing.