I have the capability to extend a class at compile time, but I need to be able to create an instance of this subclass at runtime using an instance of the superclass that was
To reiterate what you are trying to do..
Within the JVM, there exists an instance of ClassA. You would like to dynamically modify the class heiarchy of ClassA, such that a new class exists called ClassB which derives from ClassA. Then you would like to instantiate an instance of ClassB but have it's subclass implementation be that of the existing instance of ClassA. Something like a memory replacement.
You might want to look into http://www.jboss.org/javassist . What you would need to do is replace the ClassLoader, then determine when ClassA is being loaded, then instantiated. You'd then need to construct ClassB and return that instead.
Update
After a little more research there is still the possibility you can do what you want. IDE's like Eclipse support HotSwap'ing method implementations while debugging. They use the Instrumentation API.
http://zeroturnaround.com/blog/reloading_java_classes_401_hotswap_jrebel/
You can replace method bodies but not add or remove methods themselves. So while you won't be able to change the type to your new type, you can completely replace the method implementation with your new implementation.