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That could be only a fuel delivery problem, for example a clogged or incorrect main jet, or restricted fuel flow. Do you mean you replaced the fuel filters of both bikes? Is the stock filter still in at the carb fuel inlet? I think something is restricting fuel flow. That is, something from the petcock to the main jets.
On a side note, in my experience, needing needle shims indicates carbs that are not completely clean. I needed shims when I got my '05, but after Ducatiman refurbed them using the same jets and other stock parts, the shim was not necessary.
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