Based on your sample message it would appear that uuencoding the body is just going to make your flat file larger than it really wants to be. You might want to consider simply converting \n to some other control character (preferably one that won't be appearing on its own in an email) so that it doesn't interfere with using \n as a delimiter in the file.
you might try \a, since forgetting to change this back to \n will ring the bell, which should keep people from using cat to look at the files more than once... *grin*