GST query for B2B

I have some queries regarding GST. (Actually many :-) )

1. I read somewhere that freight and packaging charges must also be added under taxable value before issuing invoice to retailer. Is it true? Actually the thing is that I am a B2B supplier and currently in our business we bear the transportation and packaging charges on behalf of our customers. What should I do then?

2. Also I heard that I will have to issue an extra copy of invoice (instead of 2 currently) to the transporter. Also there is something called invoice reference number. I also heard that I can give this invoice reference number instead of issuing extra invoice. What is this invoice reference number? Do I need to mention this number on my each invoice? Please clarify.

3. I am wholesale cloth merchant. We mainly deal with cotton cloths. Before GST it was exempted from excise duty etc. Then what should I do with my existing stock. Many of my colleagues are saying that we need to pay return on closing tax at the rate of GST (1.e. 5%). This is biggest confusion prevailing in our community. Even many of CAs in my area aren't clear about it.

Please respond quickly.

Thanks in advance.