Bill,
I'm not totally sure I understand the disconnect here. Are you aware that in the source pane of the XPage you can simply type in normal HTML? <div></div> and all that stuff? It sounds like you might not be. You can put any valid HTML tags into the xpages source. <fieldset> is a good one for instance.
So you could create a new .nsf... that uses the latest ext. library... set the them to one of the bootstrap themes... create an xpage.. and then go do the bootstrap website and take an example and copy the html directly into your xpages source. Now if you do that some examples need to be modified slightly as the bootstrap examples are not alwars valid xml... so you might have to close some tags... or replace some characters with the xml equivalent. But that's a decent way to get started really...
Below is one of my older custom controls that's just a little navBar in an application... but just notice that you can have pure html inside the XPage. The only real "XPages" stuff in here I think are a couple of links... One link even brings back a value from a managed bean. Using a repeat control for the "hamburger" icon seems a little silly... I forget where I got that from. so don't let that confuse you. I would litterally just take the example from the bootstrap website as a starting point of building a new one.
Now some bootstrap examples have the form tag... I believe technically all of the xpage is inside a form tag by default. So whenever I get one of those examples I change the <form> to <div> and keep the css styling.
Does that help?
==========
<?xml version="1.0" encoding="UTF-8"?>
<xp:view xmlns:xp="http://www.ibm.com/xsp/core">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<xp:text styleClass="sr-only" value="Toggle navigation" />
<xp:repeat value="#{3}">
<span class="icon-bar" />
</xp:repeat>
</button>
</div>
<div class="collapse navbar-collapse">
<ul class="nav navbar-nav">
<li>
<xp:link styleClass="navbar-brand" text="Home" value="/home.xsp" />
</li>
<li>
<xp:link styleClass="navbar-brand" text="Admin"
value="/admin.xsp">
<xp:this.rendered><![CDATA[#{javascript:database.queryAccessRoles(session.getEffectiveUserName()).contains('[Admin]');}]]></xp:this.rendered>
</xp:link>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<xp:link styleClass="navbar-brand"
text="#{Exhibitor.name}" value="/home.xsp" />
</li>
</ul>
</div>
</div>
</xp:view>