I have never owned your bike (or even a bike with a chain for that matter) so these are just generic answers. I’m sure an actual owner will be along soon to give specific answers.
1. 8~9k Sounds about right. You should be able to tell by upshifting. If you feel the engine struggling to pull at that speed then you were probably in the correct gear to begin with. Higher RPMs generally mean lower mpg but unless you are just cruising down the freeway you want to be in the optimal gear for your speed.
2. Factory tool kits tend to be extremely basic pieces of crap so a regular toolkit is probably a better choice. A spanner is a spanner after all. You will want to stiffen up your suspension for a passenger and you may even want to change it for just yourself. Not sure if you need a special tool to do that on the ninja. My scooter has a weird shaped tool to do that so this might be tricky.
3. Every 500 miles is standard I think. There are special brushes and cleaning supplies to do this. Simply put it up on the center stand (if you have one) and rotate the wheel and clean the chain. Not difficult and I’m sure there will be videos out on YouTube to show you how it is done.
4. Not sure about mpg on the Ninja. That does sound a little low but it depends a lot on your riding conditions. If you are in town a lot then your mpg will plummet.