Install PuTTY on the windows machine, use PSCP to transfer files, and Plink for executing commands/scripts on the Raspberry.
From the docs:
PSCP, the PuTTY Secure Copy client, is a tool for transferring files securely between computers using an SSH connection.
Plink (PuTTY Link) is a command-line connection tool similar to UNIX ssh. It is mostly used for automated operations, such as making CVS access a repository on a remote server.