Turns out, my problem was in the hardware setup. I need better glasses/lighting. I had the external trigger hooked up to TXD1, not TXD2 which is the ADTRG. So my original code does work.
After some testing, it appears that the PIO doesn't need to be involved at all. Setting the ADC_MR_TRGSEL_ADC_TRIG0 bit seems to take care of the ADTRG, but this is not explicitly stated in the data sheet. You just have to wire it right! 
Also I don't think the frequency should matter, the rise time of the ADTRG could. But as long as the edge of the signal is there it should trigger.
Thanks for looking at this.