Need advice on tutorial of computer simulation

There's no need to program custom scoring.

Instead, put the screenshots on Graded Hotspot slides. Or use Freeform Pick One slides (https://community.articulate.com/series/articulate-storyline-360/articles/articulate-storyline-360-user-guide-how-to-convert-existing-slide-to-freeform-interaction ), which can also be automatically graded by the program. 

By default, any question slide has Correct and Incorrect layers. If you don't want to use those, just turn Feedback to None. 

If you want to provide hints, set the Attempts to any number >1. The program will automatically add a Try Again layer. 

Is it possible for the user to have to do things in a certain order? For example, they have to click this box before they click that box to get points.

Each object to be clicked would have to be on a separate Hotspot/Pick One question slide, and those slides would need to be in the proper order.

If you want to give the impression of continuing through the process, but without giving them unlimited attempts, you could use the Try Again (as I mentioned previously), and keep the default Feedback: By Question.

• On the Incorrect layer, put an appropriate message, so the user knows what they should have clicked. Use the standard Continue button that hides the layer and jumps to the next slide. 
• On the Correct layer, apply a Blank layout and remove all objects from the timeline. Add a trigger that jumps to the next slide when the timeline of the layer starts. 

If you're unsure what you want, I suggest you try various option on just 2-3 slides, until you decide how you want them to work.

Thanks so much for your help. I'll play around with it and I might have more questions later, if that's okay!