Redid it all 3 times today, Reapplied thermal paste and pressing down on the pads to make sure they are were not preventing the backpaltes from making contact.
Isn't the idea for them to make contact with the backplate, they're not going to transfer much heat if they have nothing to transfer it too.
You should try to avoid touching thermal pads or pressing them down, grease from your fingers will interfere with the transfer of heat and any deformation of the pads will mean they're not making contact with whatever your trying to sink the heat too.
You should've used a really sharp blade to cut them to the exact size you need, make sure they don't cover anything higher than what you're trying to cool as that will leave a gap between what you want to transfer the heat too. Once you've cut all the pads so they sit level on what you want to cool clean the surfaces thoroughly with isopropyl alcohol, peel off one side and carefully lay them in place, once they're all in the right place peel off the other protective covering, clean what you're going to sink the heat too (the heatsink or backplate) and gently attach it making sure not to dislodge or move the pads. Typically it's easiest/best to screw each screw until you just feel a bit of resistance and then give each screw a turn or a half so you don't squash one thermal pad more than another.