After an unexpected break I did what I didn't think I could do.
While attempting to build lv2 applications I overloaded and frustrated myself to the point that I had no desire to do anything at all for Ubuntu Studio. Two weeks or so later after I stopped working on it I find myself reintroducing myself to zynjacku.
Approaching it with a fresh perspective allowed me to review the problem again and re-evaluate some of the data which proved critical, along with reading the GNU Make manual. And it now appears that I managed to build it correctly in my Karmic PPA.
I say "appears that I managed to build it correctly" because my testing methods were not extremely conclusive, but satisfactory at this point, consisting of running zynjacku and lv2rack from the command line and adding effects. This was also tested on a fresh Ubuntu Studio install in VM. Granted, the one lacking aspect is that I didn't actually run any sound through them to test. A somewhat disturbing flaw in an otherwise rewarding experience. Once I have my recording setup resurrected (and improved) I will test it directly.
I would like to push this into REVU but one last, remaining item needs to be addressed: the desktop file. The desktop file tells the Ubuntu system where to place the application in the menus and provides an icon for it.
Unfortunately, I believe I will need more help than the current documentation (that I have found) can provide to accomplish this.
After I complete the desktop file and submit to REVU I shall document my changes to the upstream version here in this blog. And most likely will start on either zyn or lv2vocoder since they are by the same developer and should be similar.