Good vendors will have tests performed on every shipment of kava they get. My understanding is that FDA requires a certificate of analysis on every incoming shipment of a nutritional supplement as of 1 Jan 2013. This can be avoided if the exporter does some shady labeling - but I can assure you everything we have is tested.
In a nutshell, the stems and leaves will have more of the larger, undesirable molecules (DHM, etc.) as well as the possibility of other compounds, alkaloids, etc. there is the belief that the larger molecules are more cumbersome for the liver to process, and that is what may cause the damage, which is why "noble" varieties have nigh levels of kavain, a very small molecule comparatively, and others.
That said, some people seem to like the long-lasting effects of tudei or Isa or wild kavas, which is non-noble. Isa in particular was introduced to Hawaii by Dr. Lebot. When I last spoke to him, he said he brought it there insisting it was for research only. Apparently, it grew so much faster than other noble types that sellers saw money, and ignored his warnings. That said, if I understood him correctly, Dr. Mattias Schmidt does not necessarily think there is anything wrong with consuming non-noble kavas - but don't quote me on that. I have found that non-noble varieties tend to have more of a piney, evergreen-type smell than the creamy or peppery smell of the nibles. Of course, the "smell test" is not as accurate as a lab test, but I have found that the more piney smelling the kava, the more likely I will get nauseated. (and nausea is also generally a sign of the larger kavalactone molecules.)
I will be meeting with Dr. Lebot next month, and doing some filming for a documentary, and will be sure to get his thoughts and the details on that, and many other common questions about kava, in an accessible video format. In the meantime, if you are concerned, I would stick to noble variety kavas that have had confirmed NIRA testing on them to ensure chemotype. Reputable vendors should have no scruples sharing their test results. I'm looking to scan and post mine shortly, but have been really busy lately, but can promise you everything we have at Vanuatu Kava Bar/Store is "All noble, all the time."
Hope that helps! Cheers!
Alez!
~AP