I may be misreading this, but 25 courses, with 34,500 quizzes (=> over 1000 quizzes per course) - although "only" 16000 actual questions...?
Are they redundant rows left behind when the quizzes have been deleted, or do you actually have that many quizzes on those courses? If so then I think some cleaning out and then some user training might be the first thing I'd look at. Along with restricting that plugin to users who have had some kind of input about what they are doing.
That may not be the reason for the speed issues you are asking about, but it will help the usability of your course pages and the quizzes themselves no end!