Don't beat yourself up... I'm already an MD, so these clinical sort of scenarios are typical, everyday sort of things you deal with. It won't come right off the bat, it takes a little time and experience to start building those bridges and integrations. What I can tell you though is study hard but smart and start trying to make cross-system connections from early and things become a lot easier.
Btw I actually have been using Pathoma lately since I decided to sit Step 1 (exam next week.. lol). The guy is impressively good, but I'd also strongly advise having something else to back up his material when you're first learning the discipline because his main focus is to delve into the barebones high-yield and testable stuff for step 1.
Don't bother reading all of Robbin's though (except the first 6 or 7 chapters), its overkill and I doubt you'd retain much of it, if any. I gave Robbins away years ago and been using Rubin's Pathology ever since. Well written, compact, concise, all winning ingredients IMO, but it also depends on what kind of learning style fits you best. I think that right there is the biggest challenge.