There is a noticeable difference in the ports between the pre and post 09 barrels (much more than just a machine cleaning up the ports) as they are different shapes. From my own experience, the post 09 barrels have more low end grunt but a pre 09 barrel can still be faster at the circuit. If you speak to the engine builders, they know how each year's barrel tend to work, so using your example of the 04 barrel, you'd be told that generally they are lacking low down but have a very strong top end.
If you're on the old seal (ie nothing through the cylinder head cover) you can work on Brian's suggestion and take a print of the exhaust and transfer ports, and from doing that very task on a pair of 04 cylinders can confirm there is a small amount of difference in the same year of barrels just from the casting process.
As for 1.2 seconds difference, that's more likely down to the carb or the power valve, but check the reed petals too (if your seal allows!)
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