"Average GPU temperature in the torture test was 52.4 degrees Celsius with the stock fan configuration, and 53C with the top filter removed, a minor change within margin of error. Interestingly, temperature went up quite a bit with the 140mm intake fan added, up to 59.3C and 58.9C with the 120mm fans moved to front intake. This is where the the stock fan configuration starts to make sense. NZXT chose negative pressure because this allows the GPU to draw air in through empty expansion slots, rather than relying on intake from the mostly-sealed front of the case. When front intake fans are added, even ones pointing towards the GPU, this airflow pattern is disrupted and the GPU can no longer pull cool air in from behind the case."
Even with a 240/280mm AIO in there, it should still be negative pressure... do you have the area behind the PC blocked off with anything?
Try running the PC with the side panel open, see if that improves things so we know if it really is airflow or not. Do not change thermal paste as the literally first thing you do! Too much that can go wrong there especially if you don't know what you are doing. Also, did you adjust the fan curve of the GPU? You might be able to get some lower temps simply by using MSI Afterburner or other tools to increase fan speed from default to higher RPMs.