After Windows->UNIX SSH File Transfer, how do I remove the extra carriage returns from my file?

Use dos2unix to convert each transferred text file from DOS format to ISO format. For example, to remove the extra carriage returns from original_file, yielding converted_file: 
% dos2unix original_file converted_file 

In the past, when you used ftp to transfer files, you didn't have to do this conversion, because ftp did it for you. Secure ftp (sftp) does binary-binary transfers only (in the interest of security), so you must perform the conversion.