If you want to just make your own Conditions for the Affliction effect in HeroLab, there is a Customize extra that allows you to simply fill in the blanks.
As for alternate conditions, there are a few things in the Power Profiles that could help you, too. For instance, if you don't like the 1st and 2nd degree options that you could combine with 3rd degree Transform, you could use the new Limit (Third degree only) for -1/rank. Also, your custom conditions are similar to the optional conditions for Illusion from the Illusion Profile.
I don't mean to dissuade you from retooling the 3e rules or messing with the HeroLab code; if you have the skills and the drive, more power to you.
I just wanted to point out there are simpler ways just in case you haven't considered them yet.