Problem 1:

Can some body help me, how to balance the equal distribution of burnt gas among all the three cylinders and stop the poping sound as well.

Consider the Gixxer as an example ... it is a single but has 2 'outlets'. If you observe how it works ... the exhaust gases at most of the time flow through only one of the outlet while the other one is a high rev exhaust outlet.

But consider the running dynamics (i.e) the pipes are going to be at different temperatures which will still ease the gas flow differently. Also the since the exits are placed at different levels and the pressure levels will be lower differently and hence again will force air out differently.

Wish designing exhausts were easy ... Now my knowledge of thermodynamics is olddd ... but an idea I can think of is to have an expansion chamber before let-out into those pipes. I still would not recommend this ... check if you can source pipes, used or new, Leo Vince or Yoshis if it is for the sound factor.

Problem 2:

My question is should I replace my battery with higher capacity or the stock one will suffice the current installation if run all at the time. (refer attached picture)

Apart from the question as to why would you want them on (I hope you mean installed ) all the time ... you will have to upgrade the Battery.I have a similar setup, though, not just limited to lighting. A BOLT USB Charger and 2 U7 Cree headlights .... My current Amaron is just not up to the task. I'm planning to upgrade to a 9AH. But when you do this you will have to also upgrade electrical's ... Stator, RR Unit and a fuse mechanism. I don't currently have a plan drawn up ... maybe the below link will help you understand better.

Technical Article: How a Motorcycle Charging System Works - ElectroSport

All the modification done on my bike are street legal, if not then can i get it endorsed?

Legalities aside ... all those lights running on city streets will make people blind. Hopefully you have switched for all those :-) in which case apologize for being presumptuous

This is a very gray area and as per my understanding ... endorsements are changes to body color/frame/engine capacity as per my knowledge. These are considered cosmetic changes and hence are not required. Personally ... i wouldn't bother with the hassle. Knowledgeable folks can correct me if I'm wrong.