Well, I can help you with getting the stylesheet to read a processing instruction that appears before the root element. The DocBook stylesheets have a match template on document root (match="/") that selects the first element for processing, and doesn't consider anything else. This template in your customization layer will recognize your PIs at the root level, and then apply the original template:
<xsl:template match="/">
<xsl:apply-templates select="/processing-instruction('MyInstruction')"/>
<xsl:apply-imports/>
</xsl:template>
But I'm not sure what you are expecting the customization layer to do with the information. In XSLT 1.0, there is no option for dynamic loading of stylesheet modules. 8^)
Bob Stayton
Sagehill Enterprises
DocBook Consulting
bobs@sagehill.net