I just want to confirmed your setup first.
1. You pretty much removed the Extension, Help Extenstion, and Agent out of EPO. Then do a reinstall or pretty much upgrade what you have?
2. You uninstall Managment Tools from your Program List?
3. Then you log back into EPO and click onPolicy or Monitor and it will reinstall the Managment Tools?
Steps you can try...
1. Uninstall the Manamgent Tools and also the MS Visual C whatever that came with the Management Tools
2. Log back to EPO and Click on Monitor and Management Tools and it should reinstall everything
3. When you go to Policy tab make sure Compatibility is set to None
Number 2 of you question - Have you deploy the agent to the customer?
Number 3 - hopefully above fix error