idjcctrl was still present in 0.8.8 but seems to be missing (or replaced?) in git? Is there a special build option to enable idjcctrl that I missed?
Also, I get the impression that all music files played by IDJC must be encoded at the same sample rate that JACK is running at or else you can expect xruns? If so, maybe IDJC should alert the user of files whose sample rate doesn't match JACKs, similar to how it warns about bad metatags?
idjcctrl only ever worked with the default idjc profile and there is no good way to implement it for idjc in session mode. The replacement functionality does need to include playlist setting though.
The xruns are caused by excessive CPU load. 'Player Resample Quality' should be set to fast. Ideally use a less bloated distribution or upgrade your computer. You can view CPU load with 'top'.