Regarding a disease based dot, I think something that incorporates some of the aspects of our previous disease dots would be interesting. Something like doing damage initially or incorporating a strength & armor class debuff. As far as pets are concerned, if it ain't broke don't fix it. Summonin...
I do believe it has to be the eqgame.exe and not the EQ.exe which will probably try to run the patcher. Try typing "eqgame" in the window and it should take you to the file. Your description of how to edit the eqgame shortcut sounds correct.