I know this is a bit after the event and you may have a solution, but I just came across this when I was trying to figure out the same sort of thing - kindle-formatted ebooks (legal!) that I had on my PC.
It works via Dropbox. What you do is copy the files from your Kindle content folder on your PC to the Dropbox folder there and then open Dropbox on your iPad. You then try to open each file in Dropbox and will be told it can't open it, but in the top right, there's the icon for Open With and you'll find the Kindle app shown when you select it. Open in Kindle, the file will be sync'd to your Kindle library and you can then delete it from your Dropbox folder.
It will then exist separately on the iPad and your PC, so bookmarks, etc., won't be syn'd between them, but it will at least be readable.
I found an easier way to transfer your Kindle free books into ipad using iTunes and Kindle for PC. Select your ipad in iTunes under devices to access the Apps menu. Scroll down to File sharing section and highlight Kindle for PC apps. Click add to select folder on your PC that contains your Kindle books. You should see a list of your books and select the books you want to add. Note you can do CTRL-click or Shift-click to select a range of books.
Plug in iPad, open iTunes, and click on Apps tab. Scroll down to File Sharing and click on the Kindle app. Click "add ..." Go to your downloads folder and put "Kindle" in the search box. All your Kindle books will be listed. Click on the one you want, click open, book appears in Kindle Documents box in iTunes. Sync - job done.