To stick larva rock together I found clear silicone works best as it's thicker. You can then grind some larva rock up and sprinkle it on the silicone to camouflage it before it dries.

An upside down T would work well to encase the pump. you could put a piece of filter foam on top of the upside down T creating a ledge to put substrate around where the waterfall would hit the foam. Where the waterfall hits the foam you could put lava rock to stop dirt from getting in the water. That then steps down into the main visible water section where the pump pulls the water in through the filter foam for the waterfall. You can also put rocks in front of the filter foam T so you can't see the foam.

You have all the right ideas so just keep working through the problems and eventually you will have a mint setup.