Where do the two cover bolts with shoulders fit. Most photos on that show the two bottom holes. Mine don't fit in there.

What are the torque specs for the guides, tensioner and over rocker arm guides

 

I'm working off a 2010 accord shop manual as I don't have a 2014.

16 ft-lb for the tensioner arm bolt, 8.7 ft-lb for the smaller guide bolts.

The shouldered bolts look to go in the lower left and lower right holes on the pic below. Not the bolts from the bottom.

 

From your post I found that the bolts on my 2014 are three from the bottom. What is the torque on guild over the cam sprockets?

 

I typically don't worry about using a torque wrench on every bolt. If the top guide is secured to the cylinder head through plastic holes, then I'd use the 8.7 ft-lb as the vertical guide smaller bolts. My approach is to ensure the bolt is tight enough to not break or warp the part you are bolting. Through plastic I tighten by hand until snug, then 1/8 to 1/4 a turn at most extra. If I'm concerned about a bolt loosening due to vibration I'll use the weakest locktite on threads as extra insurance.