Hi Eamon,
If I understand correctly, I was having a similar problem when I was trying to put a few custom pages in my site that were totally outside of the whole Zen Cart framework.
This line in .htaccess fixed it for me:
RewriteCond %{REQUEST_URI} !^/partsrequest.php [NC]
This allowed www.mysite.com/partsrequest.php to operate normally without 404.
Hope that helps!
Sasha Shepherd
HyosungSource.com
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