Sometimes it's better to have a bigger box to hide cables and stuff. This also have 5 holes for leds or cables to poke through. To use the USB-port just snip off the extra plastic.

The lid can be used to hold some LEDs or other nice stuff, drill some holes.

The simple bumper is useful to avoid shortening the board. I sometimes prefer to use the angled connectors, and I didn't find any good protection.

Add some blu-tack to mount the ESP8266 D1 circuit board. The holes are tight so you have to press 3mm leds carefully through the holes. If needed add som crazy glue to hold them in place.