A brake is a chungHa'wI'. This doesn't mean that a brake is a thing that gets slower; it means it's a thing that causes something else to get slower. Thus, chungHa' means decelerate (something), so chung means accelerate (something). Therefore, to say The ship accelerates, you have to say Duj chunglu'. Unfortunately, no form of chung seems ever to have been used in the canon, so we can't verify this analysis.
Also note that Duj means ship, not necessarily spaceship.
We are not completely sure. In English, you don't normally talk about "accelerating" something. Instead, you generally cause it to accelerate. Thus the given definition makes it sound like you wouldn't use an object. However, as David points out above, a chungHa'wI' is clearly causing something else to decelerate, implying that something would have to cause the ship to accelerate and your suggestion of the ship itself is not a bad way to go (as well as the suggestions by David and mizinamo). But without more canon or clarification by Dr. Okrand we can't be sure and I, myself, will probably continue to use chung as intransitive for now.
Sure, English accelerate can be used transitively. See Dictionary.com. "Accelerate economic growth" and "accelerate the fall of a government" are examples they give.
If you search for "accelerate the car," you'll find lots of examples of people using it.
We just don't generally use transitive accelerate to mean making the car go faster by using its controls.