Hi Lee. I took a look at your skin, but I don't know that I understand what the problem is. It works fine in Hebrew and RTL. There's one issue I did find immediately - the header is flipped; in RTL, the logo should be on the right and the menu on the left, so you need to flip the pull-right and pull-left classes when in RTL mode. You can do that in the PHP end by checking the page direction settings in MW itself.
You mentioned you have a problem with the editor - do you mean the wikitext editor? (I didn't see problems with that) or VisualEditor? If you mean VisualEditor, we don't yet support external skins, especially ones as complex as this one just yet.