Fundemental misunderstanding

I have fundemental flaws in my understanding (or lack thereof) of Japanese. No wonder I failed my N3 exam! Something as simple at the particle "に" can cascade into endless misunderstandings. It is like a stone that I trip over and fall on my face in my journey through learning Japanese. It can turn a whole sentence on its head. For example, in my mind I translate "に" into "to" or "at." The problem is that it can also mean the opposite: "from" instead of "to." This means that it cannot be exactly translated but must be learned by example - a tedious and nerve wracking process to say the least. It requires you to alter the way you think. Perhaps the brain physically changes when this happens and new neural pathways are formed. They haven't formed for me yet. I think my brain resists this at every turn. My neurons are inflexible, cold, hard things that resist change.