If the problem is noise in the 3.3V line it is easy to test it.

Cut the 3.3V traces going to the pcie conectors in a backplane or if it cant be done due to the layout/multilayer pcb just remove the 3.3V pads in the hashboard and then feed it with clean 3.3V, if you want really clean 3.3V use a 3.3V linear regulator feed with at least 5V and with big filter capacitors at the input and output.

Not the most efficient and likelly not an aceptable solution but the power will be as clean as it can be and you will know for sure if it is worth trying to make a pcb that has lower noise on the 3.3V line or not.

That can be cobled together in less than an hour if you already have the linear regulators. I like this one: http://www.ti.com.cn/cn/lit/ds/symlink/lm1085.pdf .

Although perhaps that is exactly how you came to the idea that the problem is in the 3.3V line.