Further to my post above;
1054 - Unknown column 'p.products_id' in 'on clause'
select distinct p.products_id, p.products_image, p.products_tax_class_id, IF(s.status = '1' AND s.stores_id = '1', s.specials_new_products_price, p.products_price) as products_price from products p left join specials s on p.products_id = s.products_id and s.stores_id = '1', products_to_categories p2c, categories c INNER JOIN products_to_stores p2s ON p.products_id = p2s.products_id where p2s.stores_id = '1' and p.products_id = p2c.products_id and p2c.categories_id = c.categories_id and c.parent_id = '90' and p.products_status = '1' order by p.products_date_added desc limit 9
[TEP STOP]
I now understand the problem and this was me setting my database on a server with SQL 5.0.19 running. After version 5.0.12 the SQL syntax changed to bring it into line with the 2003 standards. This resulted in the error above as the structure of JOIN, SELECT AND ON has changed and therefore the code used above in Multi Stores will not work.
This is not meant to be critical of this superb Contribution - just a warning to any one looking to use it and also to future proof it.