I'd like to echo the OP's sentiments. I walked out of this exam feeling incredibly despondent, no where near as comfortable as I did with Step 1 (and I didn't feel that great after Step 1 to begin with). I felt confident and prepared for maybe 60-80 questions on my Step 2 CK. I repeat, I felt prepared for 60-80 questions at most. That's it. My answers to the rest of the 250 or so questions felt at best like quasi-educated speculation, and at worst, like frank shots in the dark. I also had far more "WTF is this?" type questions on this exam than I had on Step 1 as well, inquiring about fringe concepts, esoteric diseases, incredibly specific treatments, or challenging ethical dilemmas with resolutions that all seemed superficially appropriate and plausible.
Again, Step 2 CK isn't so much about knowing definitive facts as it is apprehending the appropriate clinical approach. If you're someone like me who thinks concretely and thrives on trivia-like tidbits and associations, this makes things somewhat unsettling because you don't have the same strength of your convictions. On Step 1, sometimes you just know the answer because you just know the answer. The prompt mentions something about a dihydrorhodamine (DHR) flow cytometry test? The answer must be Chronic Granulomatous Disease. You see a pathology picture of dumbbell-shaped ferruginous bodies in the lung? The answer must be asbestosis. You just don't see that type of stuff very often on Step 2. I also felt that the resources available for Step 2 aren't quite at the same level as they are for Step 1. First Aid is a great example of this. It's an absolutely essential resource for Step 1, but for Step 2, I found it lacking in many regards.
For the record, I scored 250+ on Step 1, and my main goal was to at least beat that score for Step 2. My study strategy this time around was a full, careful pass of UWorld one time with the UWorld self-assessments and all Step 2 NBME's completed before the week prior to the exam. All of my practice exams for Step 2 CK had me scoring in the high 260's, which put me at ease somewhat, because I acutely felt my grasp of the material was for more tenuous than it had been for Step 1.
As I said, I walked out of this the real thing feeling terrible. In the ensuing hours after the exam, all of the questions I was unsure about came bubbling up from my subconscious, and upon reflection, I realized that I got most of them wrong. There were at least 20 questions that I could recall being unsure of; that's not counting the questions I either couldn't remember or didn't know that I got wrong. All in all, I was very upset for the following week and had insomnia because I worried that I had scored below my baseline of Step 1, and that the result would undermine the work I had done prior. I could have very easily postponed my Step 2 exam until after applying to residency and mitigated all of this.
Here's the moral of the story: Ultimately, in spite of all of my self-doubt, I ended up scoring in the high 260's and met my goal of topping my Step 1 score. I hope this will be some consolation to others who feel as equally discouraged as I did. There is a reason people do better on Step 2 than Step 1, and you will likely conform to that trend as well. Trust your practice tests, and don't expect to feel as comfortable as you may have before.