Hey, first of all I would like to express admiration for much much work and time went into this gigantic map!
Map creation, as any kind of modding is very important to us, but there are also limits of what can be achieved with the tools at any given point of time. There are some rules to follow, when creating maps with solar forge. Those rules are mostly in place due to planetary rotation mechanic and when creating maps, one has to adjust for those limitations.
First, let's look at the star systems. When game engine recreates your map from solar forge, it requires minimal distances between star systems. I do not have a unit count out top of my head, but it looks like you are placing them too close to each other. I understand, that your idea is to create planets between star systems, and therefore you need to minimize the travel distance, however this is not something the game engine can do as of right now. We are aware of such modding requests, but I cannot give you any ETA on how soon this specific request could be handled.
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Now to your second issue, with individual planets being misaligned. This likely happens because you have not disabled the collision check. The game tries to ensure, that every planet has such an orbit, so that planets do not collide. So even if other planets may look like they are in a perfect line, their coordinates actually change as well, it's just the human eye, which cannot see it directly.
The screenshot below shows the option you need to set to true.
This however needs to be set to true for every planet, you want to have the exact coordinate from your solar forge. HOWEVER, be aware that when you use this option, you have to be sure, that the planet will not collide with another planets during rotation. The easiest way would be disable rotation all together. Otherwise place planets in a way, where their orbits will never collide.
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As a third tip I can give you, which you have not noticed yet - Sins2 does not allow overlapping phase lanes. If you look at your gigantic map, it has multiple overlapping (crossing) phase lines, but not a single one in your screenshot. This is likely to stay as it is, as it's a mandatory mechanic for planetary rotation. So when designing maps, try to avoid overlapping phase lanes, as they will not generate properly.
Hope this helps! Please let us know of any other ideas and requests you come up with during your endeavor with the Solar Forge!