I also developed a custom plugin for PDF generation, based on the DOT PDF2 plugin. And my PDFs require a few custom fonts, and for initial development, I used FOP (the production version uses XEP). However, I never touched any of the files inside the org.dita.pdf2 folder; I made all of my changes inside files in my com.xxxx.pdf/cfg/fo folders.
When I needed to specify a new font, I added a specification for it to one of my "attr" files. For example, commons-attr.xsl includes the following attribute set:
<xsl:attribute-set name="__fo__root" use-attribute-sets="base-font">
<xsl:attribute name="font-family">Arial, MyriadPro-Regular, Tahoma, sans-serif</xsl:attribute>
<xsl:attribute name="xml:lang" select="translate($locale, '_', '-')"/>
<xsl:attribute name="writing-mode" select="$writing-mode"/>
The custom font is "MyriadPro-Regular". To ensure that this font is called by FOP during PDF processing, I added the appropriate .ttf and .otf files to my C:\Windows\Fonts folder (my plugin never used FOP on Linux, so I'm not sure where to store the fonts there; for XEP, I stored them to the appropriate /xep/fonts/ directory).
So, when you deliver your custom plugin, your installer should copy the plugin files to the DITA-OT/plugins folder, copy the font files to the appropriate OS folder, and then perform the dita --install command.
Hope that helps.