One problem with replacing Eprom chips when you change exhaust systems is that if the throttle position sensor adjustment, butterfly synchronization, and air bleeds are not adjusted correctly BEFORE changing chips, minor fueling annoyances can become accentuated. These chips are programmed by the manufacturer on test bikes that are carefully set-up to Ducati specs. If your bike is out-of-spec and you use their chip, then you'll have incorrect fueling. In severe cases it will affect rideability.
Each exhaust system supplier programs their chips differently for different bike models, sometimes having one chip for a range of models to keep it simple. So the fuel map is different for different manufacturers and some bikes simply don't run as well on some chips.
Also, a complication arises when you make other changes beyond the new exhaust and chip. The manufacturer's test bike is otherwise stock, but your's may not be. For example, (at the risk of starting another contentious air filter thread) consider this:
Ducati places the superbike air filters in the air runners. This location avoids lowering the resonant frequency of the airbox (by not filling up a large portion of the airbox volume with a bulky foam filter) and avoids disturbing the airflow near the velocity stacks as well as improving throttle response by maintaining a large free air volume (giving better throttle response - which a dyno doesn't measure BTW.) between the filter location and the velocity stacks.
So unless you have installed a programmable FIM chip and done some development work on a dyno in an attempt to match the flow and resonance characteristics of your over-the-bellmouth filter you'll have to be satisfied using a chip that was developed using the stock filters. That's why the FIM distributors at Sigma Performance (
www.sigmaperformance.com) recommended using the stock filters. They emphasize that all FIM chips are made and initially tuned with the stock filters, and they highly recommend staying with the stock units.
But, let's assume for the moment that you've got a new otherwise-stock bike that was set-up properly at the factory with the stock chip, or that you've got an older bike that's seen only routine service where the fuel injection hasn't been touched. After you install the new exhaust and chip, you'll need to adjust your idle mixture with the CO (carbon monoxide) trimmer.
On later superbikes, the trimmer is a potentiometer located next to the EPROM chip socket inside the ECU. It has a range of about 3/4 turn, so be careful, if you try to turn it more, it'll break off. When you rotate the trimmer screw clockwise, the injector's duration is shortened so the mixture is leaned. Counterclockwise gives a richer fuel mixture. The default position is it's rotation mid-point. The trimmer adds/subtracts a millisecond or so to each fuel pulse over the entire RPM range. So go easy, an eighth-turn on the screw is often all that's usually needed to cure low-speed rideability problems.
On 851's, 888's, and early 916's the adjustment screw is on the outside of the computer. The screw adjuster has a range of four turns, or plus/minus two turns. The default position is in the middle of the range. When you screw the adjuster clockwise the mixture is richened. The adjuster has no end stop, so if you over-adjust the screw the trimmer just rolls over at the maximum or minimum setting, without damaging the trimmer. Each time the trimmer rolls over a tiny click is just audible.
Alternatively, you can have your dealer adjust it using a CO analyzer. The factory manual calls out 1.5% CO for a stock bike to meet emissions regulations but goes on to say that best power is realized when full-throttle CO is in the 4-6% range. Keep a record of any changes so you can return to the initial setting if need be. Check the color of the inside of your tailpipes after a few hundred miles. They should be medium to dark grey, not black and sooty.