1. Which programs should I target if I want to focus on an MBA in healthcare/pharma management? It does not matter if it is a traditional MBA program with a smattering of healthcare/pharma courses.
Well if it's the latter, then almost any top ten program has the smattering you speak of. In terms of specialization Kellogg, Duke and Wharton are top ten schools with specialization. You just have to ask yourself what you want to do with your career take a look at what the schools offer and where graduates go and then apply to those schools.
2. Is Rutgers a good school to apply to? Are there other such schools which offer a MBA specialized in pharma/health management?
Yes, if you want to work at a pharma in New Jersey and get a salary that 15% lower than what you would receive graduating from a top ten.
3. Will I be considered a non-traditional applicant from India by the B-schools, as I have a non-engineering, non-IT, non-finance background which (according to me) makes up the biggest pool of applicants from India?
Yes, given your background it would be easier to differentiate yourself from the legions of engineers coming from your country.
4. Besides getting a strong GMAT score and good essays what else do you think I should do to enhance my application?
Well given the fact that we wrote a whole book on this question, it's hard to write in a couple sentences. But to summarize: Establish strong fit with your target schools and differentiate yourself from the competition (show how you're unique).