1. Compared to the RS390 the 899 would be an oven in India. But it's also a Ducati superbike and personal sacrifices must be made if you want to ride this thing. You do get used to it but you gotta take it to some twisty roads and open it up otherwise you're just using a bike outside of its skillset. A bit like carving up a roast with a spoon. Use it for what it's intended to be and you'll fall in love, I promise.
2. Replace the stock pegs. They suck. I bought some aftermarket pegs and did it myself (not a mechanic) and it's way cheaper than buying a full rear set.
3. Clutch and front Brake Oil do discolour because of the lines if it is a new bike. Mine went black very quickly, and after a 1,000km service that staining was gone. If your bike is secondhand and done a few kilometres then look at getting the fluids replaced. I wouldn't buy a replacement clutch, just change the fluids and see what you think. The clutch is a lot stiffer than the RC390. But you get used to it.
4. Rain Mode is fine to start out on till you get your confidence up. This bike is over 3 times more powerful than your last bike. That's not to be taken lightly but you'll grow into it easily. The 899 is a great street bike. I leave mine in Sport most of the time anyway. Don't rush. Just enjoy the stages of learning your motorcycle.
5. They must be high speed bumps.
6. I get about 175km before I see a fuel light and 220km before I'm really freaking out. But my riding conditions (open roads, twisties) would be completely different to yours so please don't use that as a benchmark. It's a thirsty thing compared to little street bikes.
Welcome to the world of Ducati ownership. Like all religions, there is a certain degree of logical denial and personal sacrifice.