Hi Folks.. first post, be nice

I've had a Kindle since they first came out. My collection has grown *huge,* and comes from many different sources, with many different formats (.azw, .mobi, .lit, .htm, etc.) I also just downloaded some audio-books (*not* a big fan, but too impatient to wait for the release in ebook form)
My problem is, the display in the home page is ALL screwed up; sometimes author in the title column, sometimes "word document blah blah" in the title column, just all kinds of random awfulness; it just grossly offends my sense of organization and order. The audiobooks I pulled down all appear to be listed in an orderly fashion (title, chapter, author) on the webpage, but in the Kindle, they show up as "Episode One," "Episode Two," and so on... no indication of which book they're from.
Additionally, some of these titles apparently have a coding "hiccup" somewhere that causes the footer/header of a page to appear as well as the story text; lots of %20's and html stuff, and finally a "page #" and then back to the story text. It's a *huge* block of gibberish which really throws a monkey-wrench into the story flow.
It's really getting to the point that I'm ready to go back to paper, some days. Is there any application out there that will let me re-work the books' headers to yield a uniform display in my home pages? I don't mind the work of having to do manual editing, as long as it clears up the nightmare mishmash of differing display formats.
I've seen Sigil, and a few others, but they seem to be mostly one-trick ponies, working with only one or two formats at most. I'm looking for a "swiss army knife" that'll tackle just about anything out there. I don't care if it isn't all GUI-pretty, as long as it's effective.
Really hoping for something positive here; this is really beginning to ruin the whole thing for me.