I'll answer some of this. (As others are doing this instant, I'm sure)
Content Manager can be set to show All; Kindle Only; Amazon Only; or SD Card only.
The easiest (I've found) way to delete items
from your Kindle is to select "Show Kindle Memory Only" from the Content Manager.
Select all of the items that you want to "Delete".
Menu: "Remove Selected Items"
Pop Up Window: Move the Cursor to "OK" and click
You've now removed the items from your Kindle.
This next bit is important:
Anything you acquired from Amazon is still stored for you on Amazon's servers for eternity. If you change "Show and Sort" in Content Manager to Show All or Show Amazon Items only; all of your content is still there and ready to download to your Kindle (free-it's yours forever).
Anything you've downloaded form other sources (manybooks, feedbooks etcetera) will be permanently deleted so either have it backed up somewhere or remember where you got it so you can redownload it if desired.
I leave Content Manager set to "Show Kindle Memory Only" and sorted by "Most Recent First" for my own ease of use. It adds some clarity to my homepage. I also delete everything that I've read...Amazon keeps everything for me anyway so why clutter up my homepage when any book in my library is only 30 seconds away? (If I got it for free; I can get it for free again

).
A reset can cure many Kindle ills...try this:
Plug your Kindle into the charger. Do a soft reset. (Hold down "Alt"+"Up Arrow"+"R" at the same time). If that doesn't clear your screen, try a hard reset. Leave it plugged in: take off the back cover...there is a small hole labeled "reset" near the battery compartment...stick a paperclip in the hole until you hear or feel a click (can take a few seconds).
Hope some/any or all of this helps. Let us know what's happening.
Scott