- Shapes, sizes and positions of the various empires
- Circular distance map markers starting from Earth
- Sector designators and clockwise spiral-out pattern starting at Earth
- Color codes (purple/yellow/blue) for different eras of space exploration, again centered around Earth
- Discontinuous empires and neutral/off-limit zones (over/under borders can explain some of them, too)
- Grouping of several star/planet/starbase locations based on episode references (I only did a TOS spot check)
Discussion: Based on the extent of the TOS travels, you only go laterally out ~250 lys from Earth, and this may be correct, but I get the feeling that they may be double that far out (and I realize there is up/down vector distances). Maybe the other empire borders can stay where they are, but the explored TOS stars/planets can "squeeze" out past them where they can into unclaimed space. Or maybe, exploration has progressed more up/down cylindrically than laterally/spherically from Earth (which is very near the centerline of the galactic plane.) Now that I think about, a tall cylindrical shape or an hourglass shape makes more sense since the Federation would bump up against the other empires, so, the only way to go is up/down. Similar on how countries define air-space where everything up to some altitude is mine, maybe empires define space-space as everything straight up and down through the galactic plane is mine. The dimension of the Federation would be an irregular-shaped ~250 lys in radius by 1000 lys in total height (thickness of the galactic plane). "Squeezing out" can still occur with the border going up/down to the edge of the galaxy. And this is why a 2D map is good enough and your 25 lys sector size works! (I ramble but I love this.)
New info keeps coming with the advent of Discovery (Prequel/TOS era) and now with the new Picard series (TNG/post TNG era). You can probably keep refining it, forever, or until you go crazy, or both.

Of course, these are only the on-screen stars/planets/starbases. There could be a dozen or so more ships during each era making an equal amount of discoveries, so, it may be a lot more densely populated than any of us can image.

Don't Stop and Good Luck!

. I have two overlapping technobabble theories on how warp factors result in variable and much higher speeds using the Cochrane Variable theory (my own warp chart), and an additional theory that results in reverse time dilation at very high warp factors (coming to Trek Tech soon). BLSSDWLF came up with an excellent warp diagram based on empirical TOS episode data that showed incredible speeds (>500,000 c) at high warp factors in interstellar space. 