"Our web server was giving some errors related to the config.xml so I deleted it"
Difficult to comment further without knowing what the errors were. Having said that, I'm pretty confident that just deleting the config.xml would be the last thing you would want to try.
Most settings within the config file are managed through the QMC and any attempt to resolve the errors you encountered should first have been tried through the QMC. Can you restore to a back up of the config.xml and try that?
Can you then effect the changes you need to configure the cluster in QMC. If QMC is still showing the cluster info you previously had, try restarting the QlikView Management Service.
And to your final paragraph
"Is there any other steps I need to do in order for the config.xml to automatically recognize the Qlikview cluster and management and directory service connector?"
All of this should be done through QMC.