Happy birthday! (I guess...
You don't seem too happy..)
About her feelings, you could probably use a finite-state automaton to switch between, for example, indifferent and creeped out, but you'll lose granularity. Or you might represent her current state as an (x, y) tuple on a plane, or use a n-uple, or wathever.
I don't know how human feelings could be represented - there are lots of shades.
You don't need strange & convoluted formulas to increase the hunger/thirst/drowsiness counters - unless they make you happy - you just have to set the appropriate tresholds. For example, a few months ago while messing around with Inform I used three 16-bit integer variables, increasing them by 1 each turn (one minute). Then, when hunger reaches 480 (8 hours passed from the last meal) I would print "You feel hungry." once every 10 turns or so. At hunger 10'080 (a week) the game ended saying "You starved to death.".
You just have to set the appropriate tresholds and print more and more urgent message, with increasing frequency - and maybe add penalties to actions and morale.
About the time scale, you could use a global integer variable that contains the number of intervals of time (seconds or minutes) elapsed since the start of the game. Then each action could advance the global time by a variable number of intervals - for example, moving from a room to another room could take [sqrt(current_room.area)/mackey_speed] +-10% seconds, and each question could advances the time by [(question_length/player_writing_speed)+(answer_length/mackey_writing_speed)] +-20% seconds - or you could simply say that moving from a room to another takes 10 seconds, and each question answered between 30 seconds and 2 minutes.
I have a few questions: how does Mackey answers the player's questions? Does she talks to the player, or does she write on a terminal? Is there a terminal present in every room? Is the facility equipped with CCTV?
Even if the current scenario doesn't have much room for exposition, you may have the player stumble on files about Mackey and her family (maybe giving the option of telling her), other possible "prisoners" in the facility and the facility itself.
You could even add other "prisoners" and have them interact with Mackey and between themselves.
You could offer the player the option to put Mackey in contact with her family (or even of faking it), or drop her family in the labyrinth along with her.