I cannot reproduce "Shaundi unlocks 3 times" bug, but it sounds like you're using the "no respect requirement" mission list file without GotR. If this is the case, it'll cause various problems because the mission list file in the mod ("sr2_city_missions.xtbl") is based on GotR, and thus tries to unlock non-existing unlockables on a vanilla game.
I've made a "no respect requirement" mission list file for vanilla SR2 (download below) so please replace your "sr2_city_missions.xtbl" with it.