Some pics of how I have the arms attached, in case there's something I can change

Loosen one of the outside monitors and rotate the bracket 180 degrees. The hole on mine was offset to center.

Good tip, but that didn't make any difference. Even removing the bracket entirely and just holding the monitor up makes no difference in the height. It would have been better if the back plates that screw into the side monitors could be height adjustable when mounted to the monitor arms, instead of being a fixed shelf.

Unless there's something else I'm overlooking, it seems like it might be necessary to drill 4 slightly higher holes in the center mount so I can mount the center monitor a bit higher, since there's a bit of room to raise the side monitor arms up a bit.

Have you adjusted the height by moving the arms up or down here:

Custom Triple mount for 40" LED screens almost done!

Why not 55"?

Used to use a 50" plasma as my monitor, from 25" it seemed too close for me. Over the years its been 32", 40", 42" and 50". 40 seems perfect from this view distance for me

Yeah, the arms are as low as they can go. Wish there were a way of moving up the center just a bit, or more adjustment room to lower the arms down just a bit more.

Like I wrote, I think at this point the only solution I can think of is to take the center back mount to a hardware store and have them drill 4 more holes about .5"-1" higher so I can raise the center monitor. Then I will be able to adjust the arms upwards a bit if necessary.

Instead of drilling four more holes, which may or may not line up given you're going to have to measure the offset and provide it to them, why not find a machine shop that can "Slot" the existing holes say 1/2" on either side of it? You will have a range of adjustment then and can tweak it as you desire. Would be a real pisser to drill 4 more and be a fraction off......

Can you explain this in mre detail? Thanks.