I'd say that there's no real way to go from formats automatically with aceptable results unless you add a bit of handiwork.
I had the same issue not to long ago, a lot of .pdf, .lit and other different formatted e-books that I had downloaded to have a digital copy of the books I own on paper, most of them formatted crappily, and some nice member pointed me to the right direction through PMs, so I can't link you the specific posts.
Anyways, all you need is Book Designer, MobiPocket Creator, and any text editor that can handle .html files, Windows' own Notepad does it just fine. I think MobiPocket Creator has a HTML editor, too, so no big deal.
So, first you need to open the file in Book Designer, and there is where you will "fix" the book format so it doesn't look awful. There's a guide in the wiki, this one:
Book Designer Graphical Guide which shows the basic tricks you need, to handle titles, paragraphs, page breaks and other elements that you'll be tweaking there.
You only need to follow the guide till the 11th step (saving backup) because you're not saving the book for any SONY e-reader. After you save the backup, all left to do in that program is to go to "File", then "save as", and you have to save the book as a HTML (the field "Type" gotta say "HTML files (*.htm)").
From this point, you can follow
HarryT's MobiPocket Tutorial. This will actually cover all the steps from the beginning, but it doesn't really go into the Book Designer step too much. All you need from this guide given that you followed the Book Designer one and saved the HTML file is from the step called "Editing the HTML File" and so on.
Oh, two advices on the cover matter: After you've read the MP Creator guide you'll see that it goes on copying some HTML and pictures for the covers and other stuff. In the first guide, for Book Designer, you'll notice 9th step is "Adding a Cover", but you don't really need to add it in the file, because MB Creator will do this automatically if you link the cover picture, and you won't want your book to have the cover repeated, lol.
Second is, try to find big covers. If your Kindle is a 6' screen one, the ideal would be 600x800. Most of my covers were downloaded by Calibre (you just need to add the PDF files first and download the metadata with the cover included, then delete the book from Calibre so it doesn't mess with your new one), but those ones usually are 400x500 or less, and MP Creator will give you a warning telling that the cover is too small (this doesn't really matter but if you wanna have your book really nice and pimp'd, lol).