Hi,
First , Install the latest Fix on Deployer and DeployerResource package.
Try doing the deployment using ocmmand line. If that is working fine. Then it should work fine on UI too.
See if you have enabled proxy or any script in your browser which is causing the timeout error.
Note : The dependency related warnings need to be resolved if they are valid warnings.
#webMethods#Integration-Server-and-ESB#webMethods-General