I got the whole Annual fee refunded, so definitely ask (nicely) and just push the point of 90 days plus (if you can). I did a feedback form response and highlighted all the trouble I had and it seemed to work, but remember to start off nice.
A positive thing is that I have now received my bank statement and it has credited the 115k (Although not appearing on Qantas yet).
For those who have had the annual fee, or half the annual fee refunded, did you request a refund when you filled out the feedback form or just set out everything that has happened and wait and see what they offered when they responded? I've phoned 9 times over the last couple of months and think that setting everything out is probably a better option now.