I know one thing for sure: The "Print PDF" is NOT exactly what adcoms see. I noticed that a lot of things I entered in the AMCAS do not show up in "Print PDF", for instance "Lecture Only" vs. "Combined Lecture and Lab". That is a required question for every class, but it does not show up anywhere. There are two HTML summary pages (one with and one without course numbers) and there is "Print HTML" and "Print PDF", but that shows up NOWHERE except the page where you actually enter the class.
So I asked my friend who is a student member on the admissions committee at (am I allowed to say what school?). She said they DO see "Combined Lecture and Lab" and it is also very important to them.
So my question would be: What aspect of the application are you wondering about?
Are you worried about mojibake in your PS or activities? I think that may be what you are worried about, because you mentioned pasting everything into notepad, and I think you would do that in order to see if it fudges things and creates mojibake. Like when you try to type entrée and it shows up as entr$@e instead. In that case, I suspect you are fine so long as it looks good on "Print PDF", but you absolutely should not trust my judgment, I have no idea. I can't really see why it would look good on Print PDF and then break before the adcoms see it. Try pasting entrée into the AMCAS - it will break immediately, it will not hide it.