I would like to stop and take a step back here so we're all on same page. We have 3 individual problems to overcome.
1. Adhering EMI shield to the PCB Board.
@EGS had a solder joint on top left corner. Mine was only held on by pink goop. How will you hold EMI shield in Place?
I haven't modified mine, since I don't have an overheating issue, but in summary:
1. The board has clips into which the EMI shield fits, that should be enough to hold it in place as long as you don't stick a heavy heat sink on it.
EGS had a blob of solder which secured the EMI shield even better, but that was probably to ensure a good ground (0 volts) connection. A blob of solder on diagonally opposite corners would ensure it can not fall off, however I don't recommend this unless you are an expert at soldering.
Kamkar has added some foam, I guess between the heatsink and GPS module clamp?, which will assist in holding the EMI shield on and pressing the thermal paste joints firmly together. I think this is a good idea, probably a bit of silicone rubber might be better than foam.
2. I bought a Copper Plate .8mm Thick - Did you purchase these too? And if so what thickness?
--- How do you plan to adhere the Copper Plate if you purchased one? Will you adhere to the underside of EMI Shield with Solder or Epoxy? Or will you cut out a hole in the EMI Shied for the SOC to poke through. Then mount Copper Plate to the Heatsink?
2. EGS has a home made 0.8mm thick copper plate, Kamkar has nothing. I like EGS's plate, it is a good size for spreading the heat across the heatsink, which will add some cooling.
You should use a very thin layer of good quality thermal paste both sides of the plate, and under the heatsink.
Cutting a hole in the EMI shield is probably a bad idea, it is going to cause extra problems to solve, such as what is going to hold the heatsink in place.
To attach the copper plate to the EMI shield, solder is probably best, but unless you are an expert in soldering then I recommend copying EGS and using a blob of epoxy glue on each corner. Make sure you don't put the glue on thermal paste, because that will not work. An alternative would be to use a nail punch to put some indents in the top of the EMI shield around the copper plate so that once assembled it can't slide out of position, you can then just assemble in order, cpu - paste - copper - paste - EMI shield - paste - heatsink - rubber spacer.
3. How do you intend to mount the heatsink to the EMI shield and/or SOC?
A very thin layer of good quality thermal paste under the heatsink, then fix the heatsink in place with a few blobs of epoxy around the edge. Kamkar has used solder instead of epoxy, but he knows how to solder and has the right equipment.
Before you put the epoxy on, apply a clamp to squeeze together the copper, EMI shield and heatsink together, apply the epoxy and then leave it 24 hours to set. A weight could be used as a clamp but would be less convenient. If any paste squeezes out when you clamp it, leave it there in case it is needed to be drawn back in when the clamp is removed.