You didn't mention what year your bike is. The DOHC models used a constant vacuum carb, which ran better with the stock airbox, assuming everything is stock inside your carbs.
Is it possible that the jets were changed when you were running with pods? More airflow through the carb means bigger jets to supply more fuel to match the extra airflow. Going back to the stock box means less air, which means bike is probably running rich. Pull the plugs and see if they look a bit sooty. If so, then you're running rich. You can temporarily turn in the mixture screws to lean it out a bit, until you check on the jet situation.
Vacuum leak: possibly, but about all you can check for is a loose band clamp where the carbs match up with the cylinder head, or maybe the input ports used for carb synchronization. Some of the DOHC bikes had/have a fuel manifold vacuum valve, which allows fuel while the engine is running. The vacuum line for that goes from Carb #2 to the vacuum valve. If that's cracked, then cylinder #2 would be running rough, but I believe the other 3 would be OK.
I hope this helps. Oh, and welcome to the forum. :-)
Luke M
Used to have a 1979 CB750L, sold it as a parts bike, now riding a slightly modified 1984 VT700C. Network/Field Engineer. Central OH, USA, Earth, Sol System, Milky Way Galaxy, Universe.
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