First thanks for reviving a classic.

I just played it a bit.
At the junkyard,  I was unable to climb down the ladder to the hole. I just could take it...
I also wasnt able to put the ladder back to the hole.
So more or less im stuck now.

How i remember it you first have to get down there, and later on take the ladder...

You can replace the ladder after you fall into the area after going upstairs. Just remember to grab it after you go upstairs to use it to get into the ship. Get the reactor while you're down there.