I'm gonna be frank
You may have tons of problems removing the pci-e pins, the board maybe very thick, or have a big ground plane who will disspipate the needed heat to melt the solder, you must use an vacuum pump, the copper wick will never be able to empty all the holes, you may need some very small pcb drill bits
It may be over your heads with this problem, you wont have any garantie that it will work as new again even putting an new pci-e connector, you may have broke some very small pcb traces etc ... and mobos are minimum 4 layers or even 8 layers thick, with pcb traces you will never see ...
I do some mobo repairs like recapping etc ... i have many different drill bits sizes under 1.5 mm ... you have to be fast and precise, and never put any physical stress on pcb traces ...