As you point out, a perfect square is still limited because it’s a square; it’s perfect qua square but not perfect simpliciter. But a source of all things would have nothing to limit it in this way, so it would be perfect simpliciter, having all perfections in an unlimited way.
I’m not speaking of a source of all things in the sense of a temporal source, e.g. the singularity that preceded the Big Bang giving rise to everything after it, but a metaphysical source, that which is more fundamental than everything else. A temporal source would only have to be powerful (and maybe not even that, because in what sense is a singularity “powerful”?), but that which is foundational of everything else would have nothing to limit it and would be perfect.
As for the other other problem, that’s not a problem because that’s one of the options I gave, that there is no source of all things. There could just be a few powerful things, a few gods or quantum fields or physical laws, with no explanation of their existence. That seems irrational to me, but I guess there’s nothing logically impossible about it.
This would imply that moral evil is not an imperfection, in which case it’s not “sin” (missing the mark) to commit evil. But I wouldn’t want to be in the position of arguing that there’s nothing wrong or imperfect about, e.g., torturing people for fun.
I suspect there’s some deeper disagreement here between us that explains the disconnect. I’m not entirely sure what it is, but maybe it’s that you disagree that morality is in any way objective? (In which case, if there’s a “source of all things”, it would be neither ‘good’ nor ‘evil’ but would transcend those human-subjective categories altogether, as I suggested earlier.)