Yes I couldn't have got it more wrong! Thanks for the pointer Mike. Just in case it helps anyone:
1) I left out the reference to skin/common_files/js/ajax.minicart.js
2) I think the div structure needs to include:
<div class="menu-minicart">
<div class="minicart">
your code
</div>
</div>
3) Finally I have moved my code into mincart_total.tpl which is important as when the refresh is called this is the file that's loaded in.