Just another day in the Shack

UPDATE – Per Stiv’s answer below, there was in fact a mistake in the fourth row, eighth column of the diagram. Fixed diagram has replaced the errant one.

I work at the logistics base for a major remote research station in…well, I’m not supposed to say. Let’s call Artanctica. It’s a great job most days, because most messages are scheduled and routine. But today Hopkins is out, and that jerk Sandusky locked up the disk with the decoding program and is on his hourly 55 minute long smoke break. (I know, I know…it’s written in COBOL and nobody knows how to maintain it or replace it.) So of course an urgent message arrives…

Captain Arbuthnot said he’s going to transfer me to Ice Station Frasier-Heine if another urgent message doesn’t get addressed pronto, so I’m hoping you can help. I do know the decoding program does not require any input other than the transmitted file, so I think everything you need is in there.

Hint 1:

Hint 2:

Hint 3:

Hint 4:

Hint 5:

Hint 6:

Hint 7:

Hint 8:

^{Notes – ##TO BE READ##:}

^{The puzzle is entirely contained within the image; the text beforehand is purely for flavor – don’t waste your time attempting to analyze its wording!}

^{For any colorblind solvers, the vast majority of the puzzle is black, gray or white. The center of each 3×3 box is colored with a red/yellow checkerboard pattern, all of which have upper left corner red. The remaining coloration is in the 3×3 box in the upper left corner. In this box, the upper left, upper right, and lower right corners are white and violet, the upper center is black and green, the middle left is black and orange, the middle right is black and red, the lower left is black and yellow, and the lower center is black and blue.}

^{This puzzle was inspired by Stiv’s recent Captain Clumsy masterpiece, and is but a humble homage. I hope you enjoy!}

Edit: please find below a text representation of the squares. The vertical lines, top to bottom, 1=black, 2=gray:

0000 0100 0010 0100 0010 0010 0100 0100 0010
0000 0010 0100 0010 0100 1000 0010 0100 1000
0000 0100 0100 0100 0100 0100 1000 0010 0100

0000 0100 0000 0010 0010 0010 0010 0010 0000
0000 0100 0000 1000 1000 0100 1000 0100 0000
0000 0010 0000 0010 0100 0100 0100 0100 0000

0000 0010 0010 0100 0010 0010 0100 0010 0010
0000 0100 0100 0010 0100 1000 0010 1000 1000
0000 0100 0100 0010 0100 0100 0100 0100 0100

0000 0100 0000 0100 0010 0100 0100 1000 0000
0000 0010 0000 0100 1000 0010 0010 1000 0000
0000 0100 0000 0010 0100 1000 0010 0010 0000

0000 0100 0010 0100 0010 0010 0010 0100 0010
0000 0010 0100 0100 0100 1000 1000 0010 1000
0000 0100 0100 0010 0100 0010 0100 0010 0100

0000 0010 0000 0010 0010 0100 0010 0010 0000
0000 1000 0000 1000 1000 0010 1000 1000 0000
0000 0010 0000 0100 0100 0010 0100 0010 0000

And the horizontal lines, top to bottom:

000 000 000 000 000 000 000 000
000 100 000 101 100 100 100 011
000 010 000 000 001 011 001 100
000 001 000 010 010 000 010 000
                                
000 000 000 000 000 000 000 000
000 010 100 100 100 100 100 100
000 101 011 011 011 001 011 001
000 000 000 000 000 010 000 010
                                
000 000 000 000 000 000 000 000
000 100 000 100 100 101 100 010
000 010 000 011 001 000 001 101
000 001 000 000 010 010 010 000
                                
000 000 000 000 000 000 000 000
000 010 100 010 100 011 100 100
000 101 011 101 011 100 001 010
000 000 000 000 000 000 010 001
                                
000 000 000 000 000 000 000 000
000 100 000 100 100 100 100 101
000 010 000 001 001 010 010 000
000 001 000 010 010 001 001 010
                                
000 000 000 000 000 000 000 000
000 010 100 010 100 001 010 011
000 101 011 101 011 110 100 100
000 000 000 000 000 000 001 000