Did you renew the pipe-to-head gaskets? If reused they commonly don't seal then leak air at decel to pop in the pipe as the engine afterburns. Common for people to think lean but can do that if RICH too, if engine has not burned enough to then let the leaked air intermix to afterburn more. Same as an air pump adding more air to a cat in car to burn later in the pipe to consume all HC. Popping in pipe can be from either rich OR lean. Lean because lean burns too slow and keeps doing it in pipe, rich because may not burn all of it again to still be burning in pipe if you add an air source like manifold leak. Seen either way do it.
I see you are playing with a DOHC, the aircuts on carb stop that popping, if one bad or leaking then it pops. Look at the left side carb as sitting on bike, the two bolt cover on the side, that is where they are located, under that cover. In that case the aircut controls a second idle air restriction that gets cut off to richen the decel to not pop. An EPA thing since Honda made the idle so lean OEM. Richen up the idle mixture screws a bit and helps too.