1: “Proof of Funds”: is it okay, if I can show my savings are in India in some form of investment (and not in USA)?
CIC have defined how much money they are expecting based on the size of the family. For a family of 2 it’s $15,312 CAD
Additionally it needs to be “Liquid” like fixed deposits, savings, etc. Even mutual funds, etc will not be acceptable.
2: Police Clearance from USA and India:- (we have lived in both for more than 6 months):
Yes, please start early (I cannot stress this enough) FBI will take long. For India goto the embassy for FBI you need to get fingerprints and then submit.
If you’re wife is in India and if she also requires FBI clearance then there are companies in India that handle FBI fingerprinting
3: Reference letters
You will need a proof of work letter from each of your employer for the years of work you are claiming points for. This work experience has to match your NOC number.
4: PNP and EE
Not a problem happy to be of help 
Express Entry is a high level process to get a Canadian PR the way it works is that your application goes into a pool and based on your application you are awarded some points under the Comprehensive Ranking System (CRS). A few times a year they draw applications from this pool based on a cutoff score that they decide on. All applications above that score get invited to complete the process and get PR and all below are left in the pool for the next draw you application can only be in the pool for a year after which you have to reapply.
The reason I said Express Entry is a high level process is because it has 3 sub categories under which applications are filed. Your application would be filed under the Federal Skilled Workers (FSW) sub category. Keep in mind FSW has its own point system (Out of 100) where you have to score over 67 for your application to be valid under FSW. Only if you make those 67+ points then your application is accepted under FSW and it goes into the EE pool.
Provincial Nomination is a way to get extra pointer under EE. This requires a province to nominate you a separate process into itself. Additionally if you then do secure PR and move to Canada then you would be required to spend your first two years in that province. People who go this route can find themselves in some remote province with no job prospects so pick wisely. Getting a nomination is popular provinces like Ontario (Toronto) is pretty hard.
If something is not clear feel free to drop the community a question.