First - you are only using HnS on Vista, right ? I'm not sure what problems might happen if you run it from XP, especially if Vista is hidden from it and it can't find what it needs to modify.
Second - when you run the UI on a Vista system with HnS active, the first thing it does is tell you, and give you a huge uninstall button as your first option.
Third - it should default to Vista as default and non-zero timeout, so you must have changed it somehow. The options to modify that stuff are in phase 4, click a bullet and then the button to "carry out selected option" or somesuch description, and it will take you to menus to change the OS descriptions, change default, change timeout etc, and also give you an option to call EasyBCD to change Vista's bootloader. (change timeout=0 there only to stop Vista displaying a second (now redundant) boot menu ).
Fourth - I haven't had problems editing menu.lst, try running as administrator.
Fifth, wait around for Guru for advice about adding Linux to the menu.lst. He'll know if it's possible.
Also if you've somehow got HnS into a broken state where you can't run it and can't remove it, you'd better wait around for Guru for advice on what to remove/rename etc.