Fundamental building blocks of reality according to Buddhism?

Understanding the origin and mysteries of the physical world is considered an unconjecturable or imponderable, and it doesn't help with ending suffering, as you already know.

"Conjecture about [the origin, etc., of] the world is an unconjecturable that is not to be conjectured about, that would bring madness & vexation to anyone who conjectured about it.
AN 4.77

Was the Buddha omniscient and knew everything? No. He definitely knew and understood everything related to the Dhamma (the teachings), but he did not know everything simultaneously.

The Buddha stated that it is not possible to be all-knowing all at once.

That means it is possible for the Buddha to know and understand all things if he tried to learn it, but not simultaneously. This means he has the capacity (the intelligence) to know all things, but it doesn't mean that he indeed knew all things.

Also please see Buddha's omniscience.

“Sir, I have heard this: ‘The ascetic Gotama claims to be all-knowing and all-seeing, to know and see everything without exception, thus: “Knowledge and vision are constantly and continually present to me, while walking, standing, sleeping, and waking.”’ I trust that those who say this repeat what the Buddha has said, and do not misrepresent him with an untruth? Is their explanation in line with the teaching? Are there any legitimate grounds for rebuke and criticism?”

“Vaccha, those who say this do not repeat what I have said. They misrepresent me with what is false and untrue.”

“So how should we answer so as to repeat what the Buddha has said, and not misrepresent him with an untruth? How should we explain in line with his teaching, with no legitimate grounds for rebuke and criticism?”

“‘The ascetic Gotama has the three knowledges.’ Answering like this you would repeat what I have said, and not misrepresent me with an untruth. You would explain in line with my teaching, and there would be no legitimate grounds for rebuke and criticism.
MN 71

Then the king said to the Buddha, “I have heard, sir, that the ascetic Gotama says this: ‘There is no ascetic or brahmin who will claim to be all-knowing and all-seeing, to know and see everything without exception: that is not possible.’ Do those who say this repeat what the Buddha has said, and not misrepresent him with an untruth? Is their explanation in line with the teaching? Are there any legitimate grounds for rebuke and criticism?”

“Great king, those who say this do not repeat what I have said. They misrepresent me with what is false and untrue.” .....

Then the king said to the Buddha, “Sir, might the Buddha have spoken in reference to one thing, but that person believed it was something else? How then do you recall making this statement?”

“Great king, I recall making this statement: ‘There is no ascetic or brahmin who knows all and sees all simultaneously: that is not possible.’”

“What the Buddha says appears reasonable.
MN 90

Sandaka, take a certain teacher who claims to be all-knowing and all-seeing, to know and see everything without exception, thus: ‘Knowledge and vision are constantly and continually present to me, while walking, standing, sleeping, and waking.’ He enters an empty house; he gets no almsfood; a dog bites him; he encounters a wild elephant, a wild horse, and a wild cow; he asks the name and clan of a woman or man; he asks the name and path to a village or town. When asked, ‘Why is this?’ he answers: ‘I had to enter an empty house, that’s why I entered it. I had to get no almsfood, that’s why I got none. I had to get bitten by a dog, that’s why I was bitten. I had to encounter a wild elephant, a wild horse, and a wild cow, that’s why I encountered them. I had to ask the name and clan of a woman or man, that’s why I asked. I had to ask the name and path to a village or town, that’s why I asked.’

A sensible person reflects on this matter in this way: ‘This teacher makes such a claim, but he answers in such a way. This spiritual life is unreliable.’ Realizing this, they leave disappointed.
MN 76

So what are the fundamental building blocks of scientist?

As for the Buddha Dhamma, they are Craving and Not-knowing, the builder of everything. By removing those blocks, the unconditioned is gained.

I have a feeling that what you call "fundamental building blocks of reality" -- i.e. atoms -- are a matter of cultural (and technological) bias.

And that for ancient Babylonians the "fundamental building blocks of reality" might have been the details of trade routes or commercial contracts; or for ancient Polynesians the "fundamental building blocks of reality" might have been details of winds and ocean currents and seasons.

"Atoms" are an explanation of (or model derived from) various technological experiments -- starting in the 17th and 18th centuries with chemistry, and gradually going on to high-energy physics at the turn of the 20th century.

I'd argue it's not a "fundamental building blocks of reality" any more than public health is (epidemiology), and all the other branches of knowledge -- unless that's how you define the words "reality" and "fundamental" (which it seems you do).

Anyway, "atoms" are an explanation for various experimental experiences -- for example the Geiger–Marsden experiments -- and I presume that without such experiences the theory of atoms, atomic theory, doesn't arise.

Anyway, according to Buddhism the fundamental building blocks might be called dhammas; or possibly dhatus. Or others, Buddhism has many ways to analyse reality, sub-divide it into components, to find out what causes what and so on.

Subatomic particles' having a "wave-particle" nature (as you mentioned in a comment) is (I would say) not a "nature" but a view -- a model, a theory -- not wrong but not especially fundamental except for people who are trying to describe some of the observation made in Physics labs.