On your paint problem I can't be much help. This usually happens because of damp -- please get a damp expert to make sure that there isn't any damp lurking in your walls. I had this once when I had pipes leaking inside the walls. I didn't know that. The other alternative is something like painting before the plaster is dry or some kind of chemical mismatch. I do know you will have to scrape all the mucky powdery stuff away and start again, at least on those areas. Don't try to seal and prime and repaint until you know exactly what the problem is and how to fix it.

Don't spend the money to match the exterior finish of the cabinetry on the cabinet interiors, you want the interiors to be easy to clean and a light material so you can see what is inside them. No one will notice or care if the interiors match the exterior (these days it is pretty much industry standard that they do not match) If the cabinet doors have glass fronts then definitely match the exterior or use a pop of paint color on the cabinet backs.

Really like the counter top combination. To create a finished look (rather than a haphazardly thrown together look), you should probably use the same color on both vertical spaces -- the same color as is between the diamond shapes on the wall.

What a beautiful house, Shahbaaz! I live in a similar house - a 150-year-old colonial bungalow in Kumaon. You have already received lots of excellent advice from better-qualified people, so all I would say is, keep its age and heritage character the central theme. The white tiles do clash, I am afraid ... flooring with terracotta tiles would echo the roof and look lovely. The columns and the arches over the doors and windows are amazing. But I'd say, leave it all chuna-painted - there's a beauty and softness to it. Don't let the painters add too much neel (indigo) in the limewash -- in the hills where I live, they put far too much if I don't watch out and the result is a harsh white. Natural lime has a softer, creamy look.