java.lang.Exception: Public keys in reply and keystore don't match

The issue here is the alias you used while importing the certificate which is similar to the one you used while creating the JKS store. Just change the alias and it will solve your issue. The source document [1] needs to be corrected accordingly.

[1] http://docs.oracle.com/cd/E19509-01/820-3503/ggfgo/index.html

The link in your question explains how to create an SSL keystore for a server, which is not what you want to do. What you did was:

1. Create a new key pair
2. Add a trusted certificate to the keystore
3. Add another trusted certificate to the keystore
4. Try to import the SSL certificate of the server as a certificate for your key pair

Step 4 fails because the SSL certificate was generated for a completely different key pair.

The three certificates are probably:

1. The SSL certificate of the webservice
2. The CA certificate that signed the SSL certificate
3. The root certificate that signed the CA

What you have to do now is to add a trust anchor to your truststore (by default: ${JAVA_HOME}/jre/lib/security/cacerts), with the result that your client accepts the SSL certificate of the webservice.

Usually the SSL server sends the whole chain except for the root certificate to the client during SSL handshake. This means that you have to add the root certificate to your truststore:

keytool -import -keystore ${JAVA_HOME}/jre/lib/security/cacerts -file CCA_Certificate.cer -alias theCCARoot

Additional steps are necessary if the webservice requires SSL client authentication, but you have never mentioned client authentication, so I assume that it is not necessary.

In the 4 point (where you are getting error : keytool error: java.lang.Exception: Public keys in reply and keystore don't match) where you are importing the certificate, please change the alias. The alias should not be npci_client_testore as it is already used for alias of keystore.