Ok, I'm done drawing. I redrew did Φ and Ψ using the Latin Υ as a template. Now they're better in terms of those limitations you mentioned and they scaled up without distorting. I used your own Σ and I also erased two pixels off of Δ to make it look more legible -- it looked suspiciously close to a D, I think. Lastly, I made a slight change to the level signs, because the letter π was too close to the letter Ε -- in level 13 I actually had to erase a line at the bottom of the text to make it more legible, which I noticed you've also done in your versions of those signs, so I guess it isn't a bad thing. You can download them here.
P.S.: I also changed a word in one of the strings, so I'm including you that file as well.