I just went hunting and finally found it.
Some obvious changes to protect the innocent.
@echo off
set username=admin
set password=Notachance
set firewallip=fw.mydomain.com
echo config vpn certificate local > fgscript.txt
echo.edit fw.mydomain.com >> fgscript.txt
echo.set private-key ^" >> fgscript.txt
copy fgscript.txt + c:\sslcerts\fw\fw.mydomain.com-key.pem fgscript.txt
echo ^" >> fgscript.txt
echo.set certificate ^" >> fgscript.txt
copy fgscript.txt + c:\sslcerts\fw\fw.mydomain.com-crt.pem fgscript.txt
echo.^" >> fgscript.txt
echo.end >> fgscript.txt
echo.config system global >> fgscript.txt
echo.unset admin-server-cert >> fgscript.txt
echo.end >> fgscript.txt
echo.config system global >> fgscript.txt
echo.set admin-server-cert fw.mydomain.com >> fgscript.txt
echo.end >> fgscript.txt
echo.exit >> fgscript.txt
plink -ssh %firewallip% -l %username% -pw %password% -batch -m fgscript.txt