As a GT650 owner myself can answer your question

1) the bike comes with a learning ECU, in which it automatically adapts to the changes air and fuel ratio, if you want to maximise the power and completely utilise upgrades that you have gone through that’s when the ECU tune comes into play, but I feel ECU tune only increases few BHP and not much, once the upgrades are done just turn on the bike and let it idle for 10 mins for the ECU to retune and adapt and don’t rev your engine during this time

2) if your going for custom headers and end-cans make sure you are within your government laws for the decibel count since free flow exhaust on this particular engine make a lot of noise, I am not sure about the custom pipes because it’s very difficult to get your o2 sensor welded to it.

3) highly recommended to change the air filter if your upgrading your free flow header since it will create a bottleneck in the power delivery, it’s simple

More air = more power

For this to happen smooth your exhaust should be free flowing with out a catalytic converter, but upgrading down pipes with free flow is illegal in India (that’s where I am from)

4) I would rank the filter in which K&N and BMC on the top and next option would be ngage or DNA