I have a clearsigned .gcode document that I would like to be able to deploy through the Windows Certificate Store. Is this possible? If not, are there any good alternatives?
No, you can't. The Windows Certificate Store has no support for OpenPGP, but relies on X.509 certificates. OpenPGP and X.509 certificates use a different format, although the underlying cryptographic principles are pretty much the same.
If you need to support the Windows Certificate Store, use X.509 certificates. Very likely your use case will require one issued by an already included certification authority.