3.) This is normal, all books from Amazon are named B00xxxxxx. Anything else you managed to sideload into kindle for pc.
1, 2, 4.) To fix this unregister k4pc in your manage your kindle - manage devices page. Then uninstall k4pc, delete kindlecontent, reinstall k4pc, register to amazon account, download your books from cloud. Now don't use k4pc any more other than downloading books out of cloud or reading them on computer. Import all books to calibre from kindlecontent, convert to epub, sideload to other devices that like epub. Since you sound like you done it before, insert steps to allow converting of drm books to epub. If you don't sideload to K4PC it should stay nice and clean.