Is it possible to see scripts running in Python Console - everything from tools and analysis vector to raster?
You should be able to run your python code from an IDE (for example Wing IDE) as long as your python path and QGIS libraries are properly set up. An IDE will allow you to set breakpoints where the code pauses until you tell the IDE to continue the parsing. You will also be able to monitor variables in separate windows.
The below screenshot is from QGIS code run in Wing IDE. Note the breakpoint (red dot).
Pythontutor.com does this very well.
Have you already tried pydev? PyDev is a Python IDE for Eclipse, which may be used in Python development.
in Qgis Developer Cookbook search for "IDE settings for writing and debugging plugins" http://docs.qgis.org/testing/en/docs/pyqgis_developer_cookbook/ide_debugging.html