It sounds like you're doing everything except indentifying your Linked HTML TOC in the guide section of the opf file.
<reference href="Text/your_html_file.html#anchor_name" title="Table of Contents" type="toc" />
If the Linked HTML TOC is self-contained in its own HTML file, you won't need the url fragment (#anchor_name). Something like:
<reference href="Text/your_html_TOC.html" title="Table of Contents" type="toc" />