The "it works vs. I understand why it works" gap is the one that actually separates people who can debug agents from people who can only demo them. My honest take: the understanding doesn't come from reading more — it comes from deliberately breaking things. Strip the framework, write the loop by hand once, watch where it falls apart.
One habit that accelerated this for me: when I hit a behavior I couldn't explain, I'd run the same prompt across a few different models side by side (I use MultipleChat for this) and compare how each one reasoned through it. Seeing where they diverged usually exposed which part was the model and which part was my scaffolding — that contrast taught me more than any single explanation did.
Looking forward to following the ground-up series. Are you rebuilding with a framework stripped out, or starting from raw API calls?