That's also my experience: the solder on the PCIe connectors doesn't melt well (or not at all)... the first additional plug I soldered on the backside of the board, just melted the plastic of the plug itself while the original PCB-solder was still hard... I had to plug in a PCI-cable into the plug first, to function as a heat sink. This worked more or less, but still wonder how well (or bad) the solder joined...maybe I need to redo it with a bigger Iron? What wattage did you use?
First PCB I did with a Radio Shack 40W iron with a huge perfect tip.
It worked OK was prepared for a struggle and it was.
I raised the PCB with some hot air too.
If it did not flow quickly I stopped and let the tip reheat.
I destroyed the tip and flipped on the workstation to 896F wattage unknown but 70-100 ish.
WIth the ground pins you are also fighting the top, bottom, middle gnd??? layers.
One reason I nixed the plastic, end of mostly straightened pins was much easier target.
I was also dealing with 2 long 12AWG heatsink wires per 3 pins (thourogly fluxed and pre-tinned).
I'd suggest 75+ if you have a choice, use what you have if reasonable.
I don't recommend guns but cheap spares for rude big stuff are.
http://www.homedepot.com/p/Weller-75-Watt-Soldering-Gun-Kit-7200PKS/100143633
http://www.homedepot.com/p/Weller-100-140-Watt-Soldering-Gun-Kit-8200PKS/100085564
I have an old 200/260 monster that I inherited, not too big for the power connections if ya don't lurk forever.
OBTW
Got me VRMs 70s mid80s instead of 80s, upper90s, and ker plink 0 watt ambient PCB temp.
Still just nekkid in the breeze but I added a playing card sized piece of cardboard to WB on upwind side to offset the WB obstruction.
Weeee, now I could coast on cooling till faster clock magically appears.
I still have one more speed on AC box fan.
YMMV
EDIT
If anyone is interested I had an idea for stock parts survival lunch.
I put it there as it probably applies to all nep owners not just OC folks.
https://bitcointalk.org/index.php?topic=170332.msg7727618#msg7727618