Just to follow up and report my experiences here in case it helps anybody in the future.
I finally got my points credited on 9 of June. I'm not sure if it was because of the multiple phone calls I made or contacting the rep here and on twitter.
It was another total mess when I tried to use the points to book some flights on GOL airways. It took 3 phone calls to get an agent who was able to do it for one flight and a 4th phone call to book the second flight. After all that and assurances that they had booked me into comfort economy, I called up GOL to check and was told otherwise.
Called Etihad back again and they acknowledged that it was not comfort economy but were not capable of booking it. In the end I just gave up and accepted the basic economy booking. A total of about 5 hours on the phone chasing my points and making the bookings. Etihad has some very good value partner airline redemptions but be prepared to have your patience tested and put in some time. I suggest grabbing a comfortable seat and a drink and maybe browse through some trip reports on AFF while on the phone with them. Don't believe what they tell you without confirming it and if they tell you they'll call you back, they won't. Just tell them you're happy to wait on hold.
A couple of things I learned about making GOL airline bookings which will be helpful for others. I started off reading this article here which was helpful:
Travelling to Brazil? Internal flights can be expensive.
www.australianfrequentflyer.com.au
It is incorrect in regards to basic economy and luggage allowance though. You get 1 23kg piece which is shown on the Etihad confirmation email and also confirmed when I talked with the GOL agent. The allowance does not show on the GOL website though so hopefully, I don't have any issues at the airport.
The Etihad confirmation email contains 2 record locators but neither of them are the one you need to manage your booking on the GOL website. Call them up and they will be able to give it to you. GOL agents are very nice and easy to deal with.
The manage booking section on GOL's website only appears in Portuguese. I used google chrome to translate to help me navigate it. You can call them up to help you with upgrades and seat selection though.
Comfort seat upgrades are very cheap as mentioned in the AFF article. It was about 23 reals and 37 reals for my 2 flights.