How do you know it is the back cylinder?
Apart from saying it it pops and bangs on the back cylinder, and that it is fine on tickover, you are not saying much. Does it pop and bang on acceleration or deceleration? (Does it happen when just revving the bike or only when riding?)
I used to have a few pops and bangs and then changed to hiher octane fuel and it stopped.
What are the plugs looking like if you remove them soon after a journey?
I am thinking
1. leak in vacuum… check carbs are balanced
2. Leak in diaphragm.. You mentioned you replaced them, but check them again
3. Possible short in HT leads. Remove Chrome covers from above plugs, Rev the bike in the dark and look for sparks running wild.
4. Has your exhaust possibly got a hole in it?
I am sure there are more things that can be thought of, just thought I would give a few thoughts.