Basically, any text wrapped in <span></span> tags is not included in the ToC. So <h3 class="chp">D<span="smallc"OCTORS</span> I<span class="smallc">N</span> A<span class="smallc"FRICA</span> 1814-1874</h3> gives me a ToC entry of D I A 1814-1874.
Otherwise, the builtin checker says everything is okay but deleting unused stylesheet items fails due to XML not well formed. Checking with Flightcrew located the error where I had left an extra < at the start of a line ( <<p class= ).