Just gave it a little go with only the primary of the new RF transformer in action, with the usual 50k ballast R behind it (so it's likely very low electrical Q, which BTW isn't the same thing we use Q nomenclature for in fusor-land - there it means output/input power).
With that L in the series circuit of main power, I was able to get it to oscillate at audible frequencies, as evidenced by the sound in this youtube vid:
http://youtu.be/8rSnaE0bR1E
And here's a screenshot of the data aq.
Decode for the plots. Left plot is radiation counters. Red is X rays, green is neutrons, units counts/minute (but calculated from 1 second of data per point). The background of those is higher than normal as the HV is on and the odd cosmic ray or whatever makes a little dischage even when it won't sustain. 980 cpm on the neutron counter correponds to 1 million neutrons/second. On the right plot, red is the HV voltage, green the current (10 ma limit can be seen in the first two bursts, limit set to 19 ma for the last - and you can see where the HV dropped while I set the new limit). The other lines on the right plot are a reference voltage we use to calibrate the rest of the data, and the gas pressure, which I wasn't changing deliberately, though it probably changed a little - that signal is logged before I get it, so it takes a big change in pressure to see it on the plot, as this data aq software is designed to just show me raw data, not massaged into units, so I can make sure I'm not clipping an a/d channel or whatever.
I did the initial two bursts by adjusting the ion source very near the threshold of "running", with 49.x kv and a 10ma current limit. I raised the current limit for the last one, as you can see on the plot, and it scaled, which is not the usual response; normally it's less than linear as increased current messes up focus due to space-charge effects. When oscillating like this, evidently that rule doesn't apply, interesting.
Sadly, I'm currently without a working oscilloscope down there (my other one is practically built into the wall upstairs, a real pain to move) - the good one ate a lightning bolt and I've not yet replaced it ($2k! - 2.5ghz 4ch DSO). What I'm wanting to achieve here is an oscillation rate more like what would be consonant with the ion travel times. That will be in the low RF range, you wouldn't be able to hear that. But this does point up the wisdom of having "unusual ways to notice things" (or, ways to notice unusual things), in this case, my audio from a couple of extra neutron detectors makes the oscillations obvious (each click might be a burst of neutrons, and it's obviously not-random, which you cannot see in the plots at one second per point at all).