Just talking to fuel moto and they have a tune thats really close to what my bike would need, will smooth out the surge, stop the POP! thanks for the recommendation to goto them!...great price on the power commander too!
Assuming the problem is just a tuning thing using Jamie at Fuel Moto is as close to a plug and play solution as you'll get. Power Commander is a good option for the Marelli bikes. If you find yourself need to adjust the idle after the new Power Commander and its new map are plugged in be sure to follow all the steps to get that task done.
After map and Power Commander installs (due to variability in bikes) adjusting the idle is sometimes necessary. You want it to be 1000-1050 rpm. Don't let it idle slower. Won't oil well at idle if its not that high. You can adjust the idle speed at the bellcrank on the Marelli bikes much like you would on a carb in a car. Just make sure you're adjusting the idle screw and not the fast idle screw (for when the engine is cold). Hot idle screw is a torx head you'll get to through a hole in the bottom right corner of the throttle body.
Once you've got the idle adjusted where you want it you'll then shut the bike off and under the same side cover as the ECM you'll see a 5 amp fuse. Pull that and let the bike set for several minutes. Then reinstall the fuse.
If you're still having a surging or variable idle condition the most common issue with them was leaks at the intake seals to the cylinder heads. It's also worth checking all the little gasket sealing points for the various sensors on the throttle body. These are old bikes now. That stuff will deteriorate.
Across the top of the throttle body you'll also see a pair of fuel mixture screws. Unless someone has worked on the throttle body at some time they should be sealed over. If they're not, however, you can't know what someone else might have done previously there. They can be adjusted if they're open. You can do so without the old synchronizer tool that the manuals recommend. But if they're still sealed over just leave them alone.
Another Marelli idle quirk; a not uncommon failure was an intermittent high idle issue. If that was a problem chasing it could create problems elsewhere. You'd occasionally get cylinder head temp sensors bad back then. If it's not idling higher when it's cold then when it's warmed up keep this potential issue mind. If you're not sure just unplug the temp sensor. The engine will "think" it's cold and should start at high idle. The high idle screw is the "other" screw you'll see on the bellcrank on the side of the throttle body.
If you experience what you'd describe as a "wandering" idle and nothing else seems to sort it have your dealer run the bike's VIN for old service bulletin related repairs. There was an ECM reflash to correct for wandering idle issues. Might be worthwhile to find out of your bike fell within the limits for the service recall and, if so, if it ever got done. I think I remember that predating 2001 models by a couple years. But, hey, it's been awhile....