If removing the baffle caused running problems, you're probibly setting the engine too lean in the first place.

Be sure to back the engine down from peak RPM on the rich side. I don't know if cars do the same kind of thing, but airplane engines "unload" in flight and turn a higher rpm in the air. Add in the G-forces encountered that often have a tendancy to pull fuel away from the engine, and you get the engine leaning out in the air noticeably.