it's still quite a bit of soldering if done by hand, 68 pins for the CPU socket alone. The CPU sockets are modified to fit properly so I can Understand why kipper2k is adding them himself. Not sure why the HDMI and SD Card slot connectors aren't being done by the board house, I imagine they can be a bit fiddly to do, maybe it keeps costs down.
For the connectors, The PLCC connector needs to be routed, sanded and snipped, the hdmi original connectors were not up to par so i use slightly different ones which need a little massaging to fit, and the SD connector is a pain as the 2 small holes dont really align up all the time so hand soldering is best.
Is the SD Slot holes alignment problem with the PCB drilling or the component? If it's the PCB design then it should be a relatively simple fix if it's production of the board or component it may need a change of board house or component supplier which is more of a pain. If modifying the PCB design is the answer then adapting the HDMI footprint for the new version would make sense too. It seems a bit crazy for you to be spending time mangling these parts to hand solder them.