Moral Dilemmas - Academic Game

This is interesting, but I have some comments.
The lowest age range is 18-24, but many players will probably be younger than age 18.
As Stormgate noted, ". . .to what extent did you feel ashamed during the game?" is asked twice. And many questions ask the same *type* of thing. "to what extent did you feel alert. . .?" is almost the same as "to what extent did you feel attentive. . .?" and "The game had my full attention." I was also asked many times how immersed I felt in the game.
But I simply cannot get immersed in a game that lasts for 3 minutes max. There are only 2 decisions. I felt like I had missed half the game when it was through. It needs to be at least 30 minutes long for me to really get into a game.
And, a technical problem: I managed to get myself stuck in some bushes. I had to restart the game. A word of warning: don't go poking your nose in the woods!
...And I noticed that pressing space jumps..howcome this feature wasn't used in the game? :( I love jumping in games!

For example; as a christian, I make choices according to Jesus. SoI would not perform the scenarios in your questionaire. Closest is a co-worker blamed for my actions. I would not feel bad and motivated by guilt, though I might feel it. I would be motivated by choosing to be honest and without reproach.

It's not the this is not a good thought, but your questions force the premise that people are ONLY motivated by the guilt after. and as such would have behaved in a certain way.
Most the questions I would have acted in a different way and NEVER found myself in that situation.

Really cool concept
Development of the choices will allow to slowly immerse into the game. Giving a better reflection of character and the games effects.
It seems your questions lean toward resistance to evil with Guilt the restrainer. I am more motivated by following good moral choice with Joy as reward. (not ecstasy)
Awesome concept and discussion, but humbly suggest you delve into the concept of Guilt in relation to Moral choice.
If dicussing moral choice, Religion is definitely a factor, no option. Life and Moral compass have MASSIVE impact upon guilt we face.
I Strongly suggest you factor this into your thesis (as this is for a masters)

question 43 and 44 seems to be exactly the same...? I would also prefer to have less questions and some more game-parts between the next questions.

The questionare feels more like you're trying to create statistics for an answer or bias that you already have. There isn't enough content from the game to justify the number of questions. Finally, the questions stray from any relevance to the topic rapidly and repeatedly. All said, it feels like you aren't sure what you're project is really about.