If the install path to your new store is not the same as it as in the previous store then yes you will need to modify all order anywhere links to point to the new location.
Go to Merchandising > Order Anywhere and select a product and look at the add to cart link url. That is what it will have to be changed too on you store pages. Usually you can just do a Search and Replace in a text editor and make the changes fairly quickly.
Was the login name for your old store brushy? Is that the login name on the new store? If not you will also need to get a new auth file with that as the storeid. And make sure that the serial number is the same in both stores also. You can find the Serial number for your store on the Preferences > Hosting services screen near the bottom. If that screen has been blocked by your host you can run another cgi that will display the auth file for your store. On the main ShopSite screen replace the start.cgi in the url with diagnose.cgi and hit enter. A diagnostic screen will display and your auth file will be about 2/3 of the way down the page. The last line of the auth file will be something like
http://www.yourdomain.com/store:brushy: ... 2:99990002 The yourdomain name should be the same in both the old and new auth files.
The serial number will be the first number, in this case 0001108372 The second number indicates which host you are with and the 2 at the end of the 99990002 indicates the store is a Pro level store. So if you moved to a different host and the last number is the same except for the 2 instead of 1 at the end you did not get your auth file from the new host. Note that this file is encrypted so you can't just change the last line to change the authorized url or to make it a different level, as that would corrupt the file.