I think that you would be able to change things in your templates enough to make Bobby accept it. When I run your journal URL through the report, I see a few things that you might need MT tweaking for.
You might need to tweak with the links to recent comments and pings. I think that it wants the text to be different in each link, its more descriptive, so you could add in the title into the comment link - they it could say "Sunday, news? comments (0)". And then it looks like its not liking the popup codes, so you might think about using the Individual Archive page (what you see when you click the permalink time) for comments. This wouldn't require "onclick" clicking, and it wouldn't require script in the head of the document, both of which should be more accessable.
You may also wish to play with your stylesheet to use more relative sizes for the fonts instead of fixed ones (which is what px are).
So pretty much, if you go through the Bobby Report, you should be able to make most of the changes it wants. If you get stuck on something particular, post back and one of us should be able to help

Kristine