I thought the EFI self adjusted from some various posts on the forum, is that correct?
I take it you are referring to the systems which "self-map" (and automatically re-map to compensate for engine wear, etc). No, it isn't that sophisticated. Having said that, it runs "closed loop" a lot of the time - more or less all the time you are riding around on moderate throttle, so in that sense, yes, it will compensate for any changes you make because it monitors the O2 sensor and adjusts the mixture until it is stoichiometric.
However, when you are really giving it some beans it runs open loop (i.e. ignores the O2 sensor) and rich. The amount of extra fuel it injects to achieve that extra richness comes from an internal map, which the ECU cannot update itself. So under those circumstances you can assume that the degree of richness is no longer optimum if you've changed the intake or exhaust system.
It won't be far enough away to do any harm - but it might not release all the extra performance that your new exhaust or air filter promised.
In summary: unless you're a full-throttle kinda guy, then it will be running closed loop and stoichiometric most of the time, and that won't change with a new silencer. It won't self-adjust for the new silencer at high speeds or large throttle openings, when it runs open-loop. Thus you may not get all the extra power promised by the silencer.