Is my chain too long? I'm in the process of setting up a new drive train.  When using the smaller chainring and smallest sprocket (hence least amount of utilized chain), the chain brushes up against the bottom of the derailleur. 

Should I remove a link or two until this no longer happens?
Edit: from your photos, yes, the chain is too long. In the large chainring-large cog photo it looks as though the derailleur arm could be pulled forward at least one chain link, possibly two.

My preferred method of finding chain length is to focus on the largest chainring-largest cog combination. If there's just barely enough chain for that everything will work, although the small-small combo may have a lot of slack. Park have an exhaustive explanation of various methods.

Too much chain is kind of annoying, but too little can break things. Trying to shift into the large-large gear when there's not enough chain will stop your pedals, so there's a lot of force involved. Since you're going into a lower gear at that point, it often happens when you're pedalling hard. Hard enough to snap the chain in some cases. But also to snap the rear derailleur if it can't accomodate the position required, and if you're especially unlucky you might snap off the derailleur hanger as well. This breakage often throws the derailleur into your rear wheel which both breaks spokes and can dump you on the ground.

What I suggest is shifting into the large-large combo and see if there is spare chain. Try pulling a link over itself so there's a wee Z formed in the chain. If you can do that there are extra links. Keep extending the Z until the rear derailleur seems unhappy, counting links. Now remove them. Remember you do need a little slack so you can get out of the gear - you're using the return spring in the rear derailleur to pull the chain off the biggest cog, and if there's too much chain tension it won't be able to do that. But as long as you can get into the gear you won't break anything (you just need to add a link back in, and maybe pull the wheel out to release the tension).

This ties into the "some gears man was not meant to use" discussion. In cross-over gears are the large-large and small-small ones, so called because the chain crosses over from one side of the crankset to the opposite side of the cassette. This causes extra friction and chain wear, and (almost always) those gears are duplicated elsewhere so there's no need to use them. So not being able to use the small-small combo because of slack chain should not normally be a problem.