Set it up on the stand in the upright position and the fuel tank centerline on center with the spray bar in the carb. If you can get it running well under these conditions then without touching anything install it in the plane without the cowl and try running it. It should run the same if your installation set up is correct. I would change my installation until I could duplicate the way it ran in the stand. Once that is accomplished install the cowl. Does anything change? Sometimes the air outlets in the cowl are too small and the cowl acts like an air dam and the engine will not run right until this is addressed. General rule is outlet area must be greater then inlet some say as by as much as 2 times. I have had to make and install baffles in the cowl to direct the cooling where it was needed. In one case it would not have looked scale to open up the outlets any more so instead baffles were made that not only cut down on the intake area but detected all intake air directly to the center of the cylinder and head. The engine finally ran as it should.

Good luck and keep us up to date with what you find.