I will expand the guide but I wanted to keep it basic and complete so anyone--especially those who've never done this before--can just follow it and be rooted. (and to cut down on the recurring common questions)
I did notice that the "Custom" screen does not trigger on the next boot but on the second subsequent boot, implying that the trigger occurs sometime after loading and not during bootstrap.
Synergy never triggered "Custom" for me but NoSympathy's did (but Synergy is based off of it!)
Installing the "blueui" using metamorph app (it changes the stock notification toggles to ICS blue) did trigger it on the stock rooted ROM. AFAIK
, it just modifies System.apk--but Synergy has an entirely different set of notification toggles (and I assume System.apk).
It makes me wonder if something is indeed broken or not following syntax properly which triggers "Custom".