Dan, I had posted this on the forums and also sent it in on a Support Ticket. Here's the answer I got from Marcus.

My Message:
I need instructions for a Shared Server Installation. This is my guess but you need to give exact instructions.

SHARED SERVER INSTALLATION

1) Close your store.
2) Make a backup of your database.
3) UPLOAD ALL THE FILES IN THE SRC FOLDER TO YOUR SERVER OVERWRITING THE OLD FILES.
4) RUN THE SQL scripts (in what order?) - Should the SchemaScript.SQL file be run before the DataScript.SQL?
5) REFRESH THE CACHE??

Here is his response

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Sorry that we didn't include exact instructions for shared hosting. Your instructions look correct to me. Run the SchemaScript.sql file first, then run the DataScript.sql file. Recycle your web site after everything by editing the web.config file and adding a space somewhere.

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So this is my write up of the order for Updating SP2 to SP3.1 in a SHARED SERVER setting

1) Close your store.
2) Make a backup of your database. (You may also want to make a backup of your entire Store files especially if you did any custom coding, or if you modified any of the built-in themes)
3) Upload all of the files in the /SRC Folder of the SP2 to SP3.1 Upgrade. (if you have customized any files you'll need to make backup copies and then reintegrate your custom code into the new files)
4) Using SQL Server Enterprise Manager or SQL Server Management Studio open your Store Database on your Remote SQL Server. Then using the Query Manager copy and paste the SQL Script codes from the two files in the /SCRIPT Folder of the SP2 to SP3.1 Upgrade. IMPORTANT RUN SchemaScript.sql FIRST THEN RUN DataScript.sql! (I find it is always useful to look and see if Query Manager shows any error messages after running each script. If so, copy and save them to be able to file a Support Ticket).
5) Open the Web.config file in the Store root. Add a space on some line and save it so that Store will be refreshed when you open a store Web page and Web.config is called.
6) Go to the Home Page of your store, this will cause the Web.Config to be called and will REFRESH THE CACHE getting rid of traces of the old store code in memory on the server. This is CRITICAL!
7) Open and Test your store. - You may want to check out the custom code posted the other day by which allows you to leave the store closed but still do test purchases while logged in as Administrator - see post http://forums.bvcommerce...lt.aspx?f=78&m=53128

LOCAL INSTALL

These are the instructions that come with the SP3.1 about doing the update locally. They are in the INSTRUCTIONS.TXT file that comes with SP3.1

1) Close your store.
2) Make a backup of your database.
3) Run SitePatchInstaller.exe and point it at your installation directory.
4) Go to your store and make sure everything is functioning.
5) Re-open your store.

Hope this helps

Rick