You can try using a variable that keeps track of how many questions are filled in a section, and then checking that to decide whether to display the next section. Something like:

//count of questions answered
var s1count = 0;
//question 1
if (document.getElementById('S1Q1A').checked || document.getElementById('S1Q1B').checked || document.getElementById('S1Q1C').checked || document.getElementById('S1Q1D').checked) {
  s1count++;
}
//question 2
if (document.getElementById('S1Q2A').checked || document.getElementById('S1Q2B').checked || document.getElementById('S1Q2C').checked || document.getElementById('S1Q2D').checked) {
  s1count++;
}
//and so on...

//check the count, say if section 1 has 5 questions
if (s1count == 5) {
  document.getElementById("sectiontwo").style.display = "block"; //or inline
}