Hi Sumit:
1. PCo is working fine with different server location, thankfully considering that this is one of the design principle 
2. Port 50050, one way should be fine, but you should also open the Agent Instance query port of your PCO.
Then you should try the following:
1. Get the name (and the Fully Qualified Domain Name, FQDN) of the server on which the PCO is installed.
2. Edit the Host file (assuming this is windows based) of the Server on which MII is installed and add the hostname and the corresponding IP address. You can add both the server name and the FQDN.
3. Connect from MII to PCO using the Server name.
The reason for this is that PCO will return you a WSDL with names inside and not IP address, MII will then try to resolve those name, but if you are initially using IP addresses, I would guess that you do not have properly setup FQDN.. Therefore MII will not be able to point to the right server.
Hope it helps,
Arnaud