Java mail is for mail not plain http.  Further javamail is a big jar
you have to deploy. Base64 or Base64u is a tiny little class.  You can
put it in an signed Applet or a JAWS utility to prepare the file at
the client or to unpack it from the server.

HTTP is happy to send raw binary. Consider how many thousands of files
are downloaded every day. Maybe you don't even need armouring.

So, here is the code I am using with your package.. it still converts a
few characters incorrectly. What am I doing wrong. Any help is greatly
apprecaited.

Specifically

81 -> 3F
8D -> 3F
8F -> 3F
90 -> 3F

public class Test
{

   public static final String zipCharset = "ISO-8859-1";
   public static final String utf8 = "ISO-8859-1";
   public static void main(String[] args)
   {
       String in = readFile(new File("c:\\in.zip"));
       Base64u base64u = new Base64u();
       base64u.setLineLength( 72 );  // default

       String enc = base64u.encode(in.getBytes());
      // System.out.println(enc);
       String dec = new String(base64u.decode(enc));
       writeToFile(new File("c:\\out.zip"), dec);
   }

   /*
    * Write output string to a file, encode if wanted
    */
    public static void writeToFile(File f, String str) {
        try {
            OutputStream fos;
            Writer out;
            fos = new FileOutputStream(f);
            out = new OutputStreamWriter(fos);
            out.write(str);
            out.close();
        }
        catch (Exception e)
        {
            e.printStackTrace();
        }
    }

   /*
    * Read input string from a file, decode if wanted
    */
    public static String readFile(File f) {

        StringBuffer buffer = new StringBuffer();
        FileInputStream fis;
        InputStreamReader isr;

        try {
                fis = new FileInputStream(f);;
                isr = new InputStreamReader(fis);

            Reader in = new BufferedReader(isr);
            int ch;
            while ((ch = in.read()) > -1) {
                buffer.append((char) ch);
            }
            in.close();
            return buffer.toString();
        }
        catch (Exception e) {
            e.printStackTrace();
            return null;
        }
    }
}