
- 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!