I like your idea of putting shrink tubing over the LEDs to minimize back scatter. I will try that on my current project.
I also like using the stinky liquid electrical tape, but have been thwarted on using it as often as I'd like. I have problems putting it into tight spaces. To help with that, I just bought 50 small disposable paint brushes from the big online retailer.
I've used the 3M tape frequently as well. It is particularly useful for holding wires in place along the side, top, bottom of the unit. I can't quite get it to work well for holding the lights though.
I've done that with certain lights, but not all seem to fit. I handcrafted a headlight/taillight combo for the 60 trolley using 5 mm flat top LEDs. They fit very nicely inside the exterior light frame.