I think you have made this more complex than it need to be.
In '_serverSpecificRequestScope.cfm' (project config) you can just override the JS and CSS
<cfif ListFirst(cgi.PATH_INFO, '/') NEQ "webtop">
<!--- only for web site --->
<skin:registerJS id="jquery"
baseHREF="/skin/jquery-ui-1.8.15"
lFiles="jquery-1.6.2.js"><!--- jquery-1.5.1.js --->
<cfoutput>
var $j = jQuery.noConflict();
var $ = jQuery.noConflict();
</cfoutput>
</skin:registerJS>
<cfelse>
<!--- /core/packages/lib/registerLibraries.cfc --->
<skin:registerJS id="jquery"
baseHREF="#application.url.webtop#/thirdparty/jquery/js"
lFiles="jquery-1.4.3.min.js">
<cfoutput>
var $j = jQuery.noConflict();
var $ = jQuery.noConflict();
</cfoutput>
</skin:registerJS>
</cfif>
<skin:registerJS id="jquery-ui"
baseHREF="/skin/jquery-ui-1.8.15/ui"
lFiles="jquery-ui-1.8.15.custom.js" />
<skin:registerCSS id="jquery-ui"
baseHREF="/skin/jquery-ui-1.8.15/themes/patersons"
lFiles="jquery-ui-1.8.15.custom.css">
<cfoutput>
.ui-widget {font-size:1em;}
</cfoutput>
</skin:registerCSS>
<!--- // JS LIBRARIES --->
<skin:registerCSS id="pslSkin"
baseHREF="/skin/css"
lFiles="stylesheet.css,styleSheet_structure.css,styleSheet_navigation.css" />
<skin:registerCSS id="jQueryCSS"
baseHREF="/skin"
lFiles="/js/jQuery/jquery-autocomplete/jquery.autocomplete.css,/js/jQuery/flexigrid/css/flexigrid/flexigrid.css,/js/jQuery/prettyPhoto/prettyPhoto.css,/js/jQuery/DataTables-1.7.4/css/demo_table_jui.css" />
<skin:registerJS id="jQueryJS"
baseHREF="/skin"
lFiles="/js/jQuery/jquery-autocomplete/jquery.autocomplete.js,/js/jQuery/qTip/jquery.qtip-1.0.0-rc3.js,/js/jQuery/jquery.jqprint.js,/js/jQuery/jquery.ga/jquery.ga.js,/js/jQuery/flexigrid/flexigrid.js,/js/jQuery/prettyPhoto/jquery.prettyPhoto.js,/js/jQuery/jcarousellite/jcarousellite_1.0.1.js,/js/jQuery/DataTables-1.7.4/js/jquery.dataTables.js,/js/jQuery/DataTables-1.7.4/js/dataTables.numericComma.js,/js/jQuery/DataTables-1.7.4/js/dataTables.numericCurrency.js,/js/jQuery/DataTables-1.7.4/js/dataTables.date.js" />
<!--- for type header --->
<skin:registerJS id="jquery-ga"
lFiles="jquery.ga.js" />
<skin:registerJS id="jquery-qtip"
baseHREF="/skin/js/jQuery/qTip"
lFiles="jquery.qtip-1.0.0-rc3.js" />
eg <skin:registerJS id="not-yslow-anymore" lCombineIDs="patersons,jquery-libraries,sliding_menu" />