What if you separate the binary and text files locally and transfer them in two steps. Once with forced binary mode and once with forced text mode.

I'm trying to transfer (migrate) a large number of files and directories from Unix to Windows. Most of these files are text or text based but come with numberous extensions (probably too many to figure out and to included in the preferences under Transfer). Only a few extensions need to be transfered binary. Unfortuantely if the text files are transfered binary we end up with the Unix LF rather than the Windows CR/LF.

Is there a preferred method to accomplish this?
Is there any other software that might allow specifying just the binary file extensions?
thanks