Thanks Steve and Dan,
Problem solved. As Dan suggested all I had to do was place a conditional around the inner part of adding the html lines to construct the menu items. Steve's solution is more logical and will be used in my next revision when I have more time to fully customize the app. I just didn't have time to figure out adding a layer without going thru the black box userconfig. and whether something else would break if it wasn't in the layers or basemap list.
Dan's solution involved:
/*------------------------------------*/
// CREATE LAYER ITEMS
/*------------------------------------*/
function configureLayers(){
. . .
in the bottom section insert a conditional such as
if (userConfig.layerItems.uniqueID !== 'your_map_service') {
before the
// COMPOSE HTML LIST STRING
html += '<li id="' + userConfig.layerItems.uniqueID . . .
and before the append
if (userConfig.layerItems.uniqueID !== your_map_service') {
html += '</li>';
// APPEND HTML
$('#layersList').append(html);
}