Visually I think the proposed page looks much cleaner. Moving the related questions to the side-panel looks good. Perhaps this could be made a bit shorter, and retain the "How to ask" panel?
Before the user types a question:
Before entering title http://img248.imageshack.us/img248/341/askaquestionbefore.png
Being the only thing in the sidebar, the "How to Ask" box stands out.
After reading it, the user enters a title. The "How to Ask" box is moved out the way by something else they should pay attention to, the related questions:
Mockup when user enters title http://img259.imageshack.us/img259/3810/askaquestiontitled.png
After verifying it's an original question, they start writing their question body.
Once that is done, the user scrolls down to click "Post your Question".. but they spot a big brightly coloured flashing box with plenty of
<blink> tags (okay, maybe no flashing or blink tags):
Mockup of lower part of page http://img229.imageshack.us/img229/2107/askaquestionwhensubmitt.png
Two possibilities: The question does indeed looks wrong, so the user reads the markdown primer, realises they need to add a few blank lines, and proceeds falls in love with the wonderfully simple Markdown syntax.
Alternatively: the question looks fine, because the user has experience with Markdown, from their blog or wherever - so, they click the little close button, and it is never seen again.
As a slight aside:
Issue: Offline writing then copy and paste doesn't work
With basic knowledge of Markdown, you can easily write your questions/answers in any text editor. Many editors have markdown previews, and there is even dedicated Markdown editors.
With a WYSIWYG editor, there is almost no way to write text offline, then paste it without having to reapply any formatting (at least not without lots of incredibly error prone paste-detection and auto-formatting)
Solution: Replace Markdown with a more elegant solution which understands CRLF. Even better, implement a true WYSIWYG editor if possible
It completely disagree with this. I think a simple prompt (as mentioned in the article, and mocked up in the above images) should solve this whole one-return-linebreak kerfuffle, without the need to fork Markdown..
If it doesn't look right in the preview, it's not hard to work out "I'm probably doing something wrong". The brightly coloured box, pointing the user to the formatting help, should point them in the correct direction (and should mention the "question formatting help", link for future reference)