I created a new Slave site via template replicate of Master without "share the whole site" checked, same DB as master, database prefix of {site_id}_ all following your video to share users. I did not change any of the Folders/Files default settings. My Slave site looks to have been created properly, as it copied all content into a unique /multisites/{site_id} folder, and I'm using GoDaddy which I understand supports symbol links. All patches of the Slave site and Tools look like I understand they are supposed to.

My Master domain is ctpma.com
My Slave domains are cheshire.ctpma.com & www.cheshire.ctpma.com

GoDaddy has both Master and Slave mapped to the root of the ctpma.co site to allow JMS to manage the appropriate site to render, as I understand it to supposed to work this way.

Here's the issue, which you can see for yourself using the links above. My Slave site Home page and main menu Home Link work fine and render me the appropriate template from the Master, but any other link in the Slave site renders me pages without any template, and some items don't even work at all. What could I have possibly done wrong?

As a new update to my original question, I just set Search Engine Friendly URLs = NO and the links now all appear to work. Are Search Engine Friendly URLs not supported for Slave sites?

First if you are using a shared hosting on godaddy you proabably can not defined the www.cheshire.ctpma.com/

Second when we go on the ctpma.com/ and cheshire.ctpma.com/
we received websites.
We do not understand your problem with menu and the templates.

We have clicked on several menu in the cheshire.ctpma.com website and received infos correctly displayed.

Can you provide more detail and perhaps screenshot that surround the parts of the screen that is not correct for you.
Give a detailled scenario that can be reproduced.

Normally when you work is godaddy, everything should be OK (Symbolic Link + DB sharing).

When you create a subdomain on godaddy, by default it creates a subdirectory on your domain. (ie. /cheshire).

Therefore you have to check the Symbolic Link is allowed.
If not, review the Global Configuration (logs and tmp) directory path as explained in tutorial video 6
www.jms2win.com/tutorial#jms12x-6

Once you have the Symbolic Link allowed, this mean that you can deploy your slave site into the "....../cheshire" directory.

In JMS, it is also possible to have specific templates directory.
See the files and folders parameters to ask (copy) or (special copy) to have symbolic link depending on the "thems folder" parameters - see user manual.

Try the Slave site now, I just set Search Engine Friendly URLs = YES in the Slave site. Only the Home link works properly, watch what happens for any other menu link.

cheshire.ctpma.com/

Are Search Engine Friendly URLs not supported for Slave sites?

The reason is in the way you have setup the SEF.
You are using "index.php" in the SEF.
Which SEF tools are you using.

If you are standard joomla SEF in the global configuration, you have to enable the apaches mod_rewrite and SEF.
The add suffix to URL = NO

Check also the content of the ".htaccess" file if you have modified it.

If you had a look in the HTML of the pages, you would see that the CSS path are not correct.
JMS does not touch to any content.
See your "SEF" product and its settings.

It searches for templates located in "/index.php/templates/25672/css/template.css" the is WRONG as you have the "index.php" present.
The expected result is "/templates/25672/css/template.css" (with the index.php)

Review your SEF settings.

I'm using the standard SEF that came with Joomla and have not modified the htaccess file. In the template I used to create the site I asked to have the file "copied" from the master to the slave.

Can you advsie what change I should make to either the master, slave or both htaccess files? I attached a copy.

If you read the joomla documentation, you would have seen that when you are using the Joomla SEF, you have to rename the "htaccess.txt" into ".htaccess" and use the mod_rewrite and SEF.

As you will read it in the joomla "htaccess.txt" file it contains statement to make the SEF working.

See Joomla documentation for more info
docs.joomla.org/SEF_URLs_in_Joomla!_1.5

If you want that we setup your SEF then order our billable support at
www.jms2win.com/download?page=shop.produ...35&category_id=1