Sean, you may want to shoot me after reading this ..
How about;
-begin with covering/hiding all edges. Veggie filter walls, stream walls.
-because in my opinion your stream is very nice, allow it to show-off and don't cover it with a tunnel roof to begin with.
-It doesn't really matter that a part of it is dyed cement and other half is pebbles, it looks (to me) very nice and is such a shame to cover it & hide it.
When I look at the pictures, my fingers start itching (remember, this is only my personal opinion & Icy spicy taste)
Obviously you like to be thorough and precise. Your work shows that you do give yourself a lot of time to do things properly instead of finish in a haste.
-So;
1. At the lower stream-wall on photo's, fill with soil and plant a few small plants close to the edge. You have a few ferns there already - just add soil & plants behind ferns close to the stream wall.
Then, attach small / narrow rocks on the edge to cover the liner.
2. Attach the imitation rock panel to the upper stream wall/Veggie wall and add small/narrow rocks on top on the edge.
3. Use that same method (narrow rocks) on the Veggie filter walls.
When you've done that, it will look much more natural. In my opinion the black edges & walls are too visual, when I look at your stream my attention goes direct to the edges & walls instead of the beautiful details f.ex. pebbles (and 'Buddha rock').
After doing this, when all edges are hidden, the whole stream will have a dramatically different visual effect.
Not to mention if Water Carrier is in place too
Well, what da'ya think? (preparing your shotgun or..?)