Make sure when putting the motherboard back onto the bottom part of the casing that the antenna wire is where it should be - the first time I put this back together the wire got loose and was smooshed in between the casing and the Y and Power buttons, causing them to be stiff/not work. Using the spudge should help in pushing the wire back into the slots along the inside of the case.
Putting the cable back in is the hardest part out of all of this (if you can get past the screws near the beginning). If you have a friend that you trust very much and is very gentle, another pair of hands here really will help. If you're without a friend, make sure to use some flat, angled precision tweezers to push the ribbon in with one hand (pointed tweezers will do in a pinch but you'll have to be careful - I put a small dent in the ribbon and thought I'd broke it), and then use a spudge or something in the other to push the flap down.
Also worth noting is that the ribbon for the top screen also handles the 3D - if you complete the guide and find you are unable to turn the 3D effect off, you didn't insert the ribbon enough, as I had the problem and re-inserting the ribbon fully fixed it.