There are all kinds of problems in what you are saying...
But I'll start from the end:
If you have some work that needs to be done out side the GUI thread, and that work has to be sequential, then why do you put all the stages in different threads?
Have one thread call the stages one aftter the other, instead of putting each stage in its own thread.
So something like:
1. Have your thread object take a list of the objects.
2. In run() iterate over the list and call the work functions on the objects.
3. In the gui thread just have your one worker thread notify you when it is finished.