Not sure where 541 million came from; not a round number. But, what the heck?
Your zircons either have to be small enough to be usable as gems, or they have to large enough to be immobile, or nearly so. I would suggest the latter -- make them squat obelisks 10 feet high or so.
You need several layers of data at different resolutions.
- Top level: It needs to be beautiful, captivating, mysterious.
- Second level. Illustrations of useful information, including basic optics and how to make a microscope. This level is also a rosetta stone, possibly using basic chemistry and the periodic table as the Omnilingual (See the short story by that name by H. Beam Piper) Second level illustrations reveal more detail when examined with a magnifying glass, and even more with a jewelers loupe.
- Third level. A microscopic history of technology, culminating in lasers and holography.
- Fourth level. Holographic data storage.
The levels can be intermixed: E.g. The top level illustration can be made of small -- need a magnifying glass -- illustrations. Illustrations can have hologram data embedded in frames next to them with references in the data.
Encoding should start a substantial distance into the zircon, so that you can have a fair amount of wear on the surface without destroying data.
The illustrations should not be something that looks like silver or gold. Barbarians will try to take it apart, and while zircon is tough it's not indestructible.
Obelisks are mass produced, and placed in geologically stable spots. Not all obelisks are identical, but core information is repeated often. Discovering a new obelisk is always potentially revealing.
Going the other way in size, look at making zircon poker chips. Each one has only the top levels of data. Each points to the tech just to survive better, and eventually to get a level of tech that gives them access to the hologram data storage of the obelisks.
There is some merit in making them hollow, as a light object is harder to bury. OTOH a floating object is easier to smash.
Half a billion years is daunting. Look how uncommon fossils of that age are compared to the number or original critters there were.
To give you an idea of the magnitude of the task: The rocky mountains are mostly in the 3-8 thousand feet above the surrounding plain. But in the last 40 million years or so there has been some 50,000 feet of erosion from them. They are big because they are being pushed up faster than they are being worn down.
Hawaii with it's peaks is only a few million years old. Make a list of 100 million year old islands....
Why 16th century? Technology is a true blink of an eye by your scale of events.
Put the zircons on the moon. THAT's stable. Or in orbit around Pluto, or around Saturn, but outside the rings, as the rings aren't a long term (a few million years) feature. Putting a few on each major asteroid may work too.
Consider making packages of zircon poker chips embedded in ceramic foam, of sufficiently low density that the package would survive re-entry at 50 km/s (This is typical cometary debris velocity.)
Somewhere in the oort cloud you have a self repairing machine that creates and dispatches ceramic marshmallow packages of zircon poker chips. Package density is light. You want the packages to float and get stranded on land. The ceramic eventually degrades, and exposes the pile of chips to the view.
This might have a chance of surviving a half billion years. The Oort cloud is a lot more benign, if you can lick the design issues of working at temps under 10 K. Machinery might only have to wake up for a few years every million years, make and send off it's packet, then wake up again to make sure it got delivered. One of your characters can be the AI that runs the poker chip assembly line.
If you are willing to have active intervention, a lunar based AI could monitor Earth and move obelisks around as needed. In the early parts of the story, the obelisks are accepted. Later, when they get reasonable theories of geology they see that the placement of the Knowledge Stones is too non-random. Why should so many be located and river junctions, good harbours, and easy mountain passes.