I 100% see aussie cattle dog but not basenji :/. ACD have a reputation for having harsh temperaments. They were bred to work and when they don't have a job they can be known to act out. I have met a LOT of skittish ones and with his unknown background I'm not surprised. The most well adjusted ACDs I know have a job and/or compete in doggy sports/obedience. They are crazy smart and their brain needs something to do!
That being said, I'm so glad you aren't giving up on him. I love the phrase "a good dog in progress". As long as he's not a danger to your family (including your other dogs!) the behaviors you are describing should be fixable or controllable. You might need the help of a professional trainer though. They can often come to your house and asses the situation and help you learn how to train him. It's risky to go it alone when you have a dog with so many issues. He could become worse or injure you if you misread his signals.
I am NOT a dog trainer or a behaviorist though! I work for a vet and have learned a thing or two over the years. I am ALWAYS willing to tell a client when I'm not sure how to help with a behavior issues and recommend a local professional that can help them.