I am trying to get multisites search to work with using Joomla 2.5.3 & Jms 1.2.81 using the 'share whole site' option.

Is multisites search supposed to work with the Smart Search Module or the standard Search module? The Smart Search Module returns no results while the standard Search module returns results regardless of whether the multisites search plugins are enabled or disabled.

I have both Multisites Categories & Multisites Content installed. Is this correct?

I have the Master Domain URL set to 'Master' for both plugins.

First if you selected "share whole site", I don't see the added value of the "multisites search plugin" as by definition you use the same DB with the same table prefix for several webiste.

So you have a unique content and don't need to get result of website that are on different DB with different table prefix.

The "Multisites Search" is a set of PLUGINs and not a module.
They perform the queries into the joomla article content and category content.

When a Search Module submit a search, the server call all the plugins in charge to process the search requested. All the queries perform their specific job and in our case, search in the #__content and #__categories for each website defined in the configuration of the plugin.

So this is call by any module (or component) that submit a search to joomla.
Joomla call all the "search" plugins to get individual result depending on each plugin functionality (ie. search in eShop product, search in forum, search in articles, ....)