While I was studying physics at uni, I tended to find the level of confusion in QM was ok as you were expected to be confused
but I really struggled with some of the notions involved in electromagnetic theory. To do it you have to just accept that some particles are negatively charged and some positively... but I could never see why they should be and I could never get past that hurdle to be proficient at the theory.
A surprising amount fo high-level science boils down to 'it's like this because its the only currenly sensible explanation, but we still don't understand why' - ideas of informed faith, which is in part why a lot of scientists are religious in some form.
First Plan B.... then on to C, then D....
Am I hungry?