Sounds more like it's changes in air pressure within the cowl that is affecting the metering diaphram in the carb and causing the engine to act up when in the air, which is a very common problem with side mounted carbs in some cowled installs. Try this fix, install a nipple into the air hole in the carb plate and fit a bit of fuel tubing and run it inside the fuse into the static air there and see if that solves your problem.