I have used the same theme for my multi-store, I need to change header and footer completely for my second store.
How can add 2 headers and 2 footers for my multi-store?
1)As per magento standard, Create new theme and assign that theme to the new store(which you want to change header and footer). Now just copy headed.phtml and footer.html and past it in new theme, update those file html or CSS as you want.
2) Add magento store id or code condition for header and footer.
A) using store id:
<?php if (Mage::app()->getStore()->getId() == 'yourStoreID'){ ?>
//Insert your HTML or JS Code Here
<?php } else { ?>
//insert your HTML or JS Code Here
<?php } ?>
B) Using store code
<?php if (Mage::app()->getStore()->getCode() == 'yourStoreCode'){ ?>
//HTML or JS Code Here
<?php } else { ?>
//HTML or JS Code Here
<?php } ?>
Hope above solution will work for you.