You must remember that your car maked 432odd nm on the wheels. And the box is only rated at 420nm. So the 1st 3 gears on the box is the issue. This means that the tuner needs to limit the torque in the first 3 gears. This was one of my main reasons why I went over to RK Motion. My car did the same when I was FR&R tuned.
Then I can also give you a rule of thumb. This is what we do not to brake our boxes.
When I drive in D, I drive normally. About 50-60% max throttle only. I don't use the "kick down" function in D. That can damage the box as you putting to much torque through to early (at to low rpm)
When I'm in S, that's when I will go 100%.
Same in Manual. BUT we don't hammer it under 2000rpm.
So when I'm on a open road and I drive 80km/h behind a truck, I will move the lever over to manual and gear back so that my rpm is higher than 2500. That way I'm not send all of my torque through so early.
Maybe the box weakness is down low as well? I don't know.
This is what I think what's wrong don't know if it can be though. But it might be that your flywheel got damaged? Maybe some of the gurus can comment on that statement?
Also a tune can show faults on your car quicker as you pushing it past limits.
I see you stay in Durbs. Take your car to Ricardo from RK Motion, let him drive it and have a feel of it. Find out from him what he's advice will be!
I can honestly say that as long as I drive a diesel, My cars will stay in RK Motion group! No one will ever touch my cars again!
Keep us updated!
I know if your vibration damping pulley is on its way out, it will start by making a noise. Don't know if this vibration is caused by it.