Perhaps what is unseen in under the earth. The megaliths on the surface may be either the tip of a larger thing or resting over some other structure.
The whole site can be the anti-gravity device, since the lines are perfectly and accurately connecting the stones and the construction.
The sculptures are smooth like carved in wood, but are not artistic and that is not important. The lines and the alignment though, cross the site perfectly and accurately.
3 small, light and portable tools were used: 1 bigger for cutting the quarry, 1 for moving the blocks and 1 for carving and sculpting. The "U" shape of Ed's experiments suggests this is the base of the instruments of "cutting matter" and also the "anti-gravity" device.
What is the source of energy to power the tools? How is it activated? It is noiseless. It transforms the matter, since it molds the stones and does not leave debris behind.
The anti-gravity device annulate the weigh of the whole piece, making it easily manipulated to move around.
The whole site should have a source of energy to connect and activate the devices to put to work. Like a circuit board. (See many ancient sites/temples configuration, specially those in India, Egypt and Greece)
The energy source is turned on and off. Most likely inside Ed's Quarters. Might have a sort of key, so only he could put all to work. For anybody else (thieves or ordinary guests) everything is just a pile of heavy stones and weird devices. The tools in the "Tools Room" are nothing else then disguises and are worthless, in my opinion.
The wells might be the source and Ed's quarters the control room. The distribution and internal design is so accurate that implies advanced concepts of physics and dynamics.
An underground structure connecting some points all over the site is highly imaginable and possible.
As clues, Ed's photos might indicate the main structures in the site (where he is standing and the main blocks shown and positioned in the pictures)
The perfect Cardinal alignment suggests the site is carefully build to have the sculptures casting shadows pointing to what is important:
1. Hour of the day: sunrise, sunset, during the day as the sun moves
2. Solstices and equinoxes, since some stones mark a clear inclination and alignment that I conclude is the Solstice/Equinox.
3. The gates when opened according to the angle, cast a "moving shadow" into the site. In the sunrise the 9 ton gate (9am?) and the 3 ton gate in the afternoon (3pm?)
4. The "Polaris telescope" eye has an angle downwards that will cast a shadow on something, close to noon in the equinox or solstice day. (Is it really pointing out to the Polaris star?)
The site, the books and photos are clues to direct those who can see, to put together the parts to assemble, understand and put to work the anti-gravity and stone cutting devices. And perhaps another discovery to unveil the mentioned mystery of the pyramids. Perhaps the devices he used are hidden somewhere in the site, like inside a cornerstone, underneath a megalith, in a well or underground.
There are 2 novels written by Terry L. Krohn about the secret of Ed Leedskalnin. It's worth to check them out: "The Eye of the Pyramid" and the sequel "Power of the Scepter"
Such power should be kept in secrecy. If fallen in wrong hands, the damage would be tremendous. A thief would certainly sell it to a crooked/wicked person or enemy government/terrorist group. Sure thing. Even if the right person finds it, the risk of it is stolen is significant. And even in the right hands, it may provoke serious damage in the world economy (replacement of equipment and its manufacturing chain/labor, mining, black mail). Nowaday's technology can replicate anything in industrial scale and surely will be used to build powerful weapons to shift the current balance of power among nations.