Ahh got ya, so no mods..
First thing I'd do is insure the plugs are the right ones. Don't assume the plugs you pulled out were the right ones, or the dealership sold you the right ones. I've had nothing but problems sourcing the proper plugs on the 848/1098/1198 motor.
Second thing is to determine if its a fueling or ignition problem, now that we've pretty much ruled out its not an aftermarket part which is causing the issue. My guess is, you'll find it has nothing to do with the plugs, but perhaps a loose ignition cable/bad coil, dirty injector or out of calibration/bad TPS unit. All three of those things can cause the symptoms you're describing, so that's where I'd start to look.
The TPS is easy to test, all you need to do is pop off the air box (to access the connector better) stick a multimeter on two of the three pins (you can tell which ones are which the moment you start the test), set the meter to Ohms and simply open/close the throttle. This is the quickest way to figure out if the potentiometer is functioning properly. The Ducati diagnostic tool should also allow you to re-calibrate it.
The rest is harder to test. Injectors you can clean with an ultrasonic cleaner, which are cheap. Loose cables and ignition coils are hard because they stop working randomly. You can swap components (coils and injectors) in order to see if the problem goes away as well, for sure worth checking into. Testing coils at higher RPM's is almost impossible, I'm sure if the bike starts, its working fine at lower RPM so testing them the old fashion way, isn't going to help.
So Ducati diagnostic first and then I'd simply go through the bike, re-checking things and cleaning the injectors.
