If you've been doing hard accelerations and bounced it off the red line a few times, you probably burned a valve or something.
Aside from that, check all your fuel lines to make sure they are connected properly. Also, check your vacuum lines to be sure there are no cracks. Disconnect them all and check the ends of each connection point. An older bike like yours can easily have failures in this area. It's easy to check, too.
If that doesn't help, synch your throttle bodies. Also, check your tappet clearances to be sure you don't have any of them out of synch.
If all of that fails, you can check your fuel filter and fuel pump. Again, on an older bike, these can become issues.
Last but not least, double check the fuel injectors. Service on these could be needed. Usually, Sea Foam will clear up any problems, though, so start there.
That's the short list. You already put it back to the stock ECU and factory settings so if that didn't solve the problem, then let us know how these other items worked. Just do one thing at a time, easiest to most difficult (cheapest to most expensive ) and keep us posted on your progress.
--Wag--
Aside from that, check all your fuel lines to make sure they are connected properly. Also, check your vacuum lines to be sure there are no cracks. Disconnect them all and check the ends of each connection point. An older bike like yours can easily have failures in this area. It's easy to check, too.
If that doesn't help, synch your throttle bodies. Also, check your tappet clearances to be sure you don't have any of them out of synch.
If all of that fails, you can check your fuel filter and fuel pump. Again, on an older bike, these can become issues.
Last but not least, double check the fuel injectors. Service on these could be needed. Usually, Sea Foam will clear up any problems, though, so start there.
That's the short list. You already put it back to the stock ECU and factory settings so if that didn't solve the problem, then let us know how these other items worked. Just do one thing at a time, easiest to most difficult (cheapest to most expensive ) and keep us posted on your progress.
--Wag--