This is going to be a reassuring, although perhaps confusing, post. I was reading queries tonight and someone mentioned that they were, as per my instructions from another post, querying me with a finished manuscript. And that reminded me that I had recently signed up a client who had queried me with only part of her manuscript complete. And that reminded me that I had within the last few years signed and sold two new writers based on queries that were not very strong, technically speaking, and didn't have the elements I like to see, like comp titles, but just had *something* about them that appealed to me; in one case a fun, confident voice, and in the other, good sample pages.
Now, don't misunderstand: I am not saying that you should deliberately set out to not follow instructions, as it were. But this is a confusing industry, and there's lots of conflicting information out there, and you probably have lots of on-line writer friends weighing in as well, and this is a really stressful experience anyway because you are following your dream, afterall, so I would say it's probably pretty near impossible to get everything right, for every agent, all of the time. I always compare the process to writing your college essay. When I was working on mine, far too many years ago to remember (except that I do), I had far too much input on mine, and I completely over thought the entire thing, with the result that I wrote a pretty flat, lack-luster little essay which didn't do much to tell college admissions counselors what kind of person I was. I played it safe and that hurt me in the end.
Better, I think, to be a little loosey-goosey with this stuff. If you be yourself, a little quirky, a little original, yes, you might turn somebody off. But you have a far better chance of attracting a kindred agent spirit I think, the one that loves your letter and then loves your work. Again, please don't take this as carte blanche to ignore all the advice you've ever heard when it comes to query letters. But do take it as permission to relax a little, have some fun, and yes, let your query freak flag fly.