With how all the PCI-E lanes go into the CPU nowadays, it's harder to try and pin these issues down. 2 same failures on 2 different CPUS could still sadly, as you say be down to the motherboard, GPU etc.
Sounds like a tough issue to nail down, but sadly it'll need to be done 1 step at a time. I think you might need to try GPU next, then motherboard after that
In the past, I've tended to rebuild it outside of the case to test, that can sometimes yield different results, for example if something is shorting, or being bent due to weight etc. sometimes the mounting system of a cooler can cause bending resulting in poor connections and random issues.