Some quick answers to some of your questions.
1. You can edit the highlight entry on the info page to make it meaningful to you.
2. Searching the library for a word will bring up any PDF, epub or Journal with that word in the title. If you are willing to pay for Evernote Premium, it has PDF OCR capabilities and can search through all your PDF (and Handwritten journals saved as PDF) files, and find all instances of thjat word within the files.
3. When adding files to the library you can specify the tag for that group of files, so adding 50 files at the same time you can also tag those with Project one at that time. Alternately you can open all tags, tap the checkmark, which places an open box next to each file, check the ones you want to retag and click edit tags at the bottom.
4. See 2
5. I don't know if you can search notes within the file.
6.You can use the trackball to scroll the browser, or a mouse wheel.
7.Some external apps will wake the EE from standby, the only solution is to a.)remove that app or b.) plug in at night. - You can also try turning off WiFi, a big power user.