NVM. I was able to solve it by re-arranging the mod order. Unfortunately I'm now back down to the 100m/s limit. :P

Why is Luna a separate planet, instead of a Moon of earth?

The /TSE menu is manually turned off to prevent accidental fumbling. What you need to do next time is go into "%appdata%\Roaming\SpaceEngineers\Saves\{steamID}\Proper Solar System with Asteroid Belt, Trojans\Storage\3351055036.sbm_RealSolarSystems\ConfigSettings.xml" and change <EditorAllowed>false to true.

The RealisticGravity folder will have the numbers you need to change to fix your broken speed limit. I had the large grid value set to 99 and small grid at 100. That will make the speed limits 9900 and 10k m/s, respectively. There could well be other things that were disrupted if these values were broken. You may no longer have an asteroid belt, who knows. But it's not like you can't just start a new copy to get it all back.

As to Luna's orbit, we orbit around each other, with the barycenter of the earth-moon system about 4670 km away from center of Earth. At this scale, though, with the bodies being 1:50 and their moons' distances being 1:1000, the worlds are about 20 times bulkier, meaning you're right... it's pretty much a moot point, as it's not really visibly different. But I tried to make everything as close to reality as possible.