I have a "NOTE" element that lets the author add notes and automatically
counts the Note number. I am trying to figure out when there is only one
note element, it doesn't use the <xsl:number>. I tried xsl:if, xsl:choose
and xsl:when. I keep getting hung up on determining if the count is greater

1.

I don't completely understand your requirement, so I assume
you want to print a number only if there are two or more NOTE
elements. Using the count() function shoudl do the trick, for
example the following (changed some stuff to match the source
XML you provided):

 <xsl:template match="Para">
   <xsl:for-each select="NOTE">
     <xsl:text>NOTE: </xsl:text>
     <xsl:if test="count(../NOTE) &gt; 1">
       <xsl:number level="single" format="1" count="NOTE"/>
       <xsl:text> </xsl:text>
     </xsl:if>
     <span style="width:100%; font-weight:bold; padding-left:70px; ">
      <xsl:apply-templates/>
     </span>
     <br/>
   </xsl:for-each>
 </xsl:template>

BTW both your resulting HTML and CSS are somewhat odd, for example the
position:absolute" for the prefix, and using HTML spans followed by a br
instead of a proper paragraph.