Ok, so you'll probably have noticed that there is now a normal discussion below this story, even in the queue. It is the same as the regular comment code, except for a couple small differences.
When you start a new thread, while a story is in moderation, you may designate it "Editorial" or "Topical". Editorial is for "form" comments: "I think it's too long", "Why don't you change X Y and Z" etc. Topical is for "content" comments: "I disagree. I feel we need more nachos in Congress" or what have you. Please, if you have one of each, post them separately!
Once you've posted your comment, it's subsequent thread will remain whatever type you designated. Editorial threads and Topical threads may not mingle. You can easily distinguish between Editorial comments and normal comments, as Editorial ones have a read box around the subject section, while normal ones have a blue box.
Voting, you'll see, is now just voting. 0, 1, or -1 and that's all. Comments of either type may be posted at any time, before or after voting. Once you've voted, you'll get another box on the right, listing the current score, and voting breakdown.
You'll also notice another new box on the right, containing the comment filter/sort stuff. Most of this is the same, except the first select box. That allows you to say whether you want to see Editorial comments, Topical comments, All, or the default, which is "Topical Only" in normal stories, and "All" while a story is in moderation (I really recommend this or "All" as the best choices, but have it your way).
Are there bugs? Hell yes, there are bugs. Please report as you find them. Suggestions, as always, are more than welcome. One of the potential issues that has been brought up with respect to seeing comments before voting is the possibility of a "herd mentality" effect, where it'll be pretty clear who voted what, and how well the story is doing, and that may affect the voting of subsequent readers. This system is basically on probation right now, to see if that happens, and what effect it has. If you think there is such an effect occurring, point it out, and we'll try something else.
I hope that this fixes some of the more glaring problems with story moderation, and thank you all for your suggestions and input.