Learn English – Referring to a person, should I use the capital letter for “Fascist”

I would write the first word after the period in capital case, as you did in the second sentence you wrote. The general rule of writing a word in capital case after a period is still valid even if you write a single word and then a period.

In those cases, the periods are used to give an emphasis to the single words. The pause when "reading" a period is longer than the pause used for a comma; for this reason I would not say the periods are like commas, in the examples you wrote.

The suggestion by Gary's Student to use bullet points is a good one.

If the questions must appear inline for some reason, you can number them instead:

Before we can examine the implications of neuroscience for criminal law, we must address two more fundamental questions: 1) Why do we punish criminals at all? and 2) How severely should we punish them?

With a longer inline list (perhaps three or more questions), use semicolons to separate the items. For instance:

Before we can examine the implications of neuroscience for criminal law, we must address four more fundamental questions: 1) Why do we punish criminals at all?; 2) How severely should we punish them?; 3) To what extent must punishment emphasize rehabilitation?; and 4) Should the family circumstances of criminals be considered when sentencing?

The semicolons aren't necessary for clarification, but they encourage the reader to consider each point more thoroughly by slowing down their reading of the list.