What are you connecting to using Connect-Java? As with all SSL scenarios, if you want to write your own SSL logic, at a bare minimum you need to create your own SSLContext and SSLSocketFactory. You would need to create Java KeyStore instances corresponding to Pega keystore and truststore data instances. The keystore/truststore data is stored in base 64 encoded form in pyFileSource property. You will have to base64 decode this into byte array and use java.security.KeyStore.load() method to create the Java KeyStore instance.
Before this, it will help if you can elaborate on what you are trying to do with Connect-Java and what you need 2-way SSL for.