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This has been due a hint a long time so

The puzzle is meant to be read in 3 by 3 blocks. Each 3x3 set of numbers share a certain special property that not all sets of numbers would have.

and another

Most of the numbers are completely irrelevant and can be ignored.

Jesus Christ, this is old, Here's a hint:

Wow, this is old, Here's a hint:

Jesus Christ, this is old, Here's a hint:

The numbers need to be subdivided into a grid of grids that the weird box and the 3's is supposed to indicate.

Also,

The puzzle is more supposed to be solved top down, so starting from the top is suggested.