Gaining my Virginity - some questions

OK, I am sure the above joke has been made before, and I apologize for it already. 
I am brand new to this Virgin Atlantic thing, and have just, after much research and rumination, booked my travel. I do have a couple of questions that I am hoping the experts may be able to help me with:
Background: I purchased full-fare, supposedly fully-flexible premium economy tickets and upgraded them to UC using 80,000 miles (dang, the transfer from Amex MR to Flying club was fast!)
Question 1: How come my e-ticket confirmation says "NONREF/NONRERTE $50USD CHANGE FEE?" I thought the tix were fully flexible?
Question 2: How come the confirmation also says "NO FF MILES/TIER POINTS?" I understand that by upgrading with miles I naturally won't get the UC-level miles/points, but why wouldn't I get the miles/points for the booking class I purchased?
Question 3: Does the e-ticket confirmation I received, and the fact that I can retrieve the reservation on the website mean that the flights were indeed ticketed, confirmed in UC, and quite good to go? I am just a tad concerned because I have not seen the fare purchase hit my Amex card yet.
If I sound a little nervous, it's only because this was quite a bit of money
and because it took nearly 2 hours to find flights and days with the requisite inventory - in fact, we lost a seat mid-booking and had to start all over again.
My travel experience has been exclusively on domestic (US) carriers, so researching and booking on VS has been a somewhat intimidating process thusfar.
Thanks in advance for any assistance you may be able to offer, and happy holidays.
Best,
Lewis

I am brand new to this Virgin Atlantic thing, and have just, after much research and rumination, booked my travel. I do have a couple of questions that I am hoping the experts may be able to help me with:
Background: I purchased full-fare, supposedly fully-flexible premium economy tickets and upgraded them to UC using 80,000 miles (dang, the transfer from Amex MR to Flying club was fast!)
Question 1: How come my e-ticket confirmation says "NONREF/NONRERTE $50USD CHANGE FEE?" I thought the tix were fully flexible?
Question 2: How come the confirmation also says "NO FF MILES/TIER POINTS?" I understand that by upgrading with miles I naturally won't get the UC-level miles/points, but why wouldn't I get the miles/points for the booking class I purchased?
Question 3: Does the e-ticket confirmation I received, and the fact that I can retrieve the reservation on the website mean that the flights were indeed ticketed, confirmed in UC, and quite good to go? I am just a tad concerned because I have not seen the fare purchase hit my Amex card yet.
If I sound a little nervous, it's only because this was quite a bit of money

My travel experience has been exclusively on domestic (US) carriers, so researching and booking on VS has been a somewhat intimidating process thusfar.
Thanks in advance for any assistance you may be able to offer, and happy holidays.
Best,
Lewis