Those plastic condom looking things are the light tubes that spread the light from an LED. I suppose the 20 white boards with LEDS on them are to replace the GI or something with your update. You should have 1 white board and 1 light tube for each LED you are replacing.
Quoted from Agent_Hero:Cross-post from the Heighway support thread:
My Alien was one of the Texas Pinball Festival prototype machines and I finally got around to swapping in the replacement parts, though I'm not sure where these items in the attached picture go (I have dozens more of the plastic caps not pictured):
Also, the new Xeno head seems to be active with its jaw moving (seemingly) as it should in test mode, but the tongue is not moving for me. It shows an error for a stuck switch--is it referring to the switch under the top half of its head? That switch appears to be fine.
Finally, would anyone have any ideas for a way to frame and protect the "in play" edges of the lower playfield LCD? Seems like the clearcoat in that area could chip/flake/crack.