You'll need to be able to reach your windows server from your linux server in order to connect to the bitcoind instance; if they aren't on the same network, you'll need to port-forward the port for your bitcoin daemon to the windows server from your router, and make sure that your RPC config is secure. Also, if you're hosting the windows server on a home internet connection, you probably have a dynamic IP which you will have to constantly update (manually or through software) to keep it working.
The only part in your config file that matters is this part (everything else is commented out and has no effect):
rpcuser=user..
rpcpassword=pass...
rpcallowip=*
rpcport=43556
server=1
The rpcport is the port that you need to forward to the windows server, and rpcallowip should be set to the IP address of your linux server to help prevent unauthorized access.