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There is no safe way to forcefully stop a Thread in Java. Please see Why Are Thread.stop, Thread.suspend, Thread.resume and Runtime.runFinalizersOnExit Deprecated? for more details. The correct solution would be to for the application to set socket timeouts and/or stop its threads properly.

This is dependent on the default profile being set since you run two profiles on the same machine. It appears Dmgr01 is the default so the first startManager call works fine. The server scripts sets the profilename so they work fine as well. I think the first way of doing it is just as good as the second. If you look at the code for the start*-scripts in ...

I believe you have to reinstall. But, if you are running Network Deployment (DMGR), you can keep the DM and the Node agent 32 bit. Assuming you are doing this on the same machine, just install 64 bit WAS in a different directory. During the install, select a custom profile so you just create a new Node / Server and federate it to the existing deployment ...