Honestly, it will just take time. Im only an M1 but former practicing chiropractor. I practiced in multidisciplinary practices before med school and it took me ~3 years into chiro training to really feel comfortable with DDx/Hx taking/PE and in practice was still working on things. When I started seeing a lot of patients one after another in practice is when it started to feel more natural. I am still working on it as an M1 and nowhere near where I want to be as the differentials in medical practice far surpass that of what a chiro will see (strictly MSK dx). You'll be continuing to sharpen these skills well into practice as a physician. Eventually, you will start to feel more confident in your critical thinking process where your mind just heads in certain directions subconsciously. Initially youre like how the hell can I simultaneously exude confidence, converse with a patient, develop rapport, eye contact/writing balance, know which questions to ask starting with broad down to descriptive all while developing a DDx in my head, but with time, you'll just start to know which questions to ask and which questions are irrelevant etc. and it will all flow. You don't need to worry were all in the same boat bud thats why its called "practicing" medicine. Download Figure1 its a great app you can practice your Dx skills 24/7 on your phone