I've used the Knuckle Joint Boot when I've been unable to get the original boots, they do work quite OK.
In regards to the cover over the hole for the short shaft, I've just looked for a listing, but doesn't come up in any of my handy parts books. There was a pressed steel cover, like a miniature freeze plug, pressed in to the back of the housings, excuse the grubbiness of this pic, but you can see the cover in there;-