I've got a 2009 250 that had the Athena 310 kit installed by the dealer before it left the showroom floor for the previous owner. Originally I suspect it had something like the JD to modify the fuelling, however at some stage it was removed and the stock ECU modified. The bike runs great high revs in the topend but is missing the urge that the 310 has over the 250 in the low to mid. Is there any difference in the ECUs and can a 310 ECU map be simply installed into the 250 ECU? Or has the dealer just player with the fuel setting to increase fuelling to something near enough? I have looked at the parts books and can't see a different ECU listed so was assuming the ECU must be dealer programmable. The reason I ask is I'd like to try a 310 ECU to see if it makes a difference.
I'm pretty sure the Athena 310 kits come with an ECU, so I would look into getting one, if yours is the 250 ECU. You're right that the parts manual doesn't list a 310 ECU. In fact it lists the same part # for all TE and SMR models. Someone that's done a BB kit on their 250 should be able to provide an answer...
I had the 310 put on my bike and the eecuis the same but the 310 kit comes with a piggy back ecu that plugs in.