Whenever I do level editor modding, I will randomnly get these severe, almost nauseating headaches that make me feel as if I'm coming down with something. These headaches are fortunately curable if I lie down to rest for >= 15 minutes. This also happened to me often when I was doing modding last year in 2012, so it's not a recent phenomenon or anything. It was also worse last year, to the point where I had to stay away from modding for an entire day.
Sometimes I can go for a long time without these headaches happening, but other times they happen right away. Also note that this applies to using the level editor alone - I feel perfectly fine when I'm writing code.
I think it may be an effect of overexertion of the mind due to concentrating really, really hard on making sure that all the walls line up and all the welders in corners are perfectly aligned at ninety degree angles to the perpendicular walls that they're connected to.
I get that too, but usually it's just because I'm supposed to be doing something else, so I'm procrastinating, so I get really stressed :p
Also, you know there's a 'snap to grid' thing in the level editor for helping with the kinds of things you were talking about in that last paragraph, right? If you're not using that for some reason, I have no suggestions, sorry :c