I was asked the other day if we had an x64 version of SignTool.exe. Up to date, the answer is NO. If you download the tool with Microsoft Windows SDK, you will only get the x86 version. This tool has dependencies on some x86 authenticode plug-ins, and as you sure know, you cannot load x86 dlls in x64 processes.
I hope this helps.
Alex (Alejandro Campos Magencio)