Vocab on tests is one of the biggest frustrations that I have with Japanese as well. There's what I've learned through whatever sources, and then there's test specific stuff that you're expected to know. I'd say my textbooks probably covered 3/4 of what was needed, along with a whole bunch of stuff that's not needed for that specific test. Like, I was 1/4 of the way through the N3 vocabulary when I looked at what was needed for it, because in learning N5 and N4, I picked all that up.
I guess what's particularly frustrating is that if you don't look at test specific vocab, then you'll end up not doing well. But if you do, you're just learning to the test. A lot of that vocab hasn't stuck particularly well because the context I have for it is just a couple flashcards I had to make to get exposure to the word, not something I came across in a more organic manner. My big goal is to learn the language, not just pass a test at a certain time, so it's a little less fun to cram that stuff.
What's particularly funny is that in reading childrens' books, first grade level stuff, I'm picking up a bunch of N1 ("fluent") words. So a first grader is expected to know the word, or ask a parent and then know it, but foreign learners don't need it until they're approaching fluency. Yay tests.
Hope you can get things in shape before the TOPIK test. If you only got through 60%, you're obviously going to be hurting at scoring time. My only tip there is that if you don't know something on a question, mark it in your booklet, skip it, and come back to it if there's time. If you're only going to get through ~60% of the questions, make sure they're the ones you know. It's possible you could have nailed the remaining 40% if you'd just gotten to them in time.