Congrats for the lovely present to your girlfriend!
1) I'm not quite sure there's anything you can do about this. I too find the background slightly too dark sometimes and then use a nice reading lamp that slides into my cover. If the darkness of the background in your girlfriend's case is due to blurring left over pixels from previous pages, you could change the page-refresh settings:
When reading a book, tap the bottom of the screen in the middle. A menu comes up. Tap the spanner in the right hand corner. Tap "Advanced settings" in the menu opens. Just over halfway down the settings, there are the page refresh settings: set them to refresh screen every "so-many" pages, less than the current setting.
Another possibility is to play around with the font settings (the Aa icon next to the spanner). Try different fonts, font sizes, and for some fonts the 'advanced' settings to change font weight and sharpness. This might help the contrast a bit.
2) What you describe only happens if you power off the device. It remembers the (real) book page you're on, not that you're on page 4 of 46 as per your example. But you don't need to power off the device, you can put it to sleep mode (just briefly slide the off switch in stead of holding it). Sleep mode does properly remember you're on the 4th page of 46.
3) Slow response is not something your girlfriend is doing wrong... there are some bugs and sluggishness in the new firmware (2.0.0). Kobo is working on updates and I'm sure things will improve. In the mean time, I've found I did indeed get used to the slower page turns.