You could always take a sharpie and add a stripe to the wire, easy enough to do.
Compare here for 16 pin female crimp connectors
http://www.king-cart.com/phoenixent/product=RECEPTACLES-SOCKETS+IDC+.1SP+%2526+2MM+SP/exact_match=exact
and mouser
Not sure what to do about 6 position - they do exist, see the ICSP headers, this is the only one I could find.
You don't need shrouded headers - just straight male pins, keep track of which way to install.