I learned a few important things at the 7m+12m workshop in Garching:
clean treats input models in Jy/beam and Jy/pixel qualitatively (not just quantitatively) differently. Jy/pixel images are taken to be model images exactly, where Jy/beam are... somehow interpreted differently, maybe as clean component assemblies. I don't know the details, but this is a major caution.
The tbtool is not very good for extracting data for plotting. The flags are not guaranteed to be in a sane shape, which will lead to crashes if you try tb.getcolumn('FLAG'). ms.msselect, however, allows you access to most of the normal selection routines used in clean, split, etc. It is tricky, though, because ms.select does not allow you access to the same selection. Also, while spw-based selection normally allows you to select channels, in ms.msselect it does not: instead you must use ms.selectchannel. See this example.
Details about the selection are at this URL, but the documentation is incomplete and, in places, incorrect:
http://www.aoc.nrao.edu/~sbhatnag/misc/msselection/FrequencySelection.html
(for example, chanspec is not valid in msselect, or at least it doesn't do anything)