I've been kind of worrying over this. When doing my morning review (which keeps getting longer and longer) There are of course kanji that I miss completely (Usually 5 or so) due to mixing things up, placement, etc. But there's also kanji that at first glance I don't remember, but clicking on the story button jogs it enough that I can lay them out perfectly.

Now the question I have is, how do you guys handle such kanji? Do you mark them as a miss (no) or remembered (Yes)? So far I've been marking them as remembered, but I'm wondering if I'm doing myself a disservice when doing so.

I marked them as a miss. After all, the point of RTK is ultimately to know the kanji while using real Japanese, in which no stories will be present.

Your story should normally contain the answer.
Answering a question immediately after having seen the answer doesn't practice memorization.

Therefore, no. ;P

Also, I try to be careful not to allow to much of a fudge factor. Often, I thought it was "this" kanji... and then, looking at the answer, I go "oh right, of course! I knew that...", but really, I think it's best to then hit fail... You wouldn't want to memorize your mistakes!

I don't think it matters much in the end. RTK gives you incomplete knowledge on how to use characters so you're going to have to learn more things about each one anyway, which in turn strengthens your knowledge of that character.

I've tried both ways. That is, both marking it as hard and as a fail. Can't really say either way made or broke it. I guess one thing you could ask yourself is; would I know this character if I encountered it in the 'wild'?.

Remember, it's not like it's game over if you encounter a character that you might have remembered if you had only marked it as fail instead of hard.

The way I see it, Anki takes care of the bulk of everything. The bulk, as in large quantities of relatively unrefined knowledge. It's note a huge deal if you don't remember everything perfectly due to the volume Anki enables you to learn. The little mishaps can often be taken care of case by case. That's my opinion anyway.