Hogmike,
My first presumption is that we are talking about a CVO here, if that is not the case disregard most of information from here on.
Harley no longer supplies flash upgrades for this type of change on a CVO, what it means is you will have to buy a tuning mechanism such as MasterTune, SuperSert, PowerCommander etc. From there they take a base map and add fuel, timing and fiddle with stuff to get you out of the already lean condition the bike had from the factory. Even if you didnt add the open breather (stage1) and pipes or slip ons it would still be recommended to throw some fuel at the motor.
Since you have added an open breather and slip ons you have taken an already lean motor and made it even leaner, not a good thing. Recommend not riding it very far and getting it tuned with a SERT / etc. Do not get sucked in by a dealer just wanting to put a map in your bike and not actually tuning it. This process should take 5 or more hours to complete.
What gets changed, the Volumetric Efficiencies (VE) tables get changed, spark (timing gets changed) air fuel if in closed loop will probably get changed, deleanment or the fuel pump may get changed, fly by wire parameters may get changed if you have those etc etc. The volumetric tables usually need to be corrected so that the proper fuel gets sent as to what is being requested by the ECM based on the loaded map. Harley's timing tables are usually very very conservative and you can understand why some areas have 85 fuel some have 93 and a mix all over the countries, and then you have the ethanol in the fuels which makes them even more difficult to deal with.
If all I did was muddy the waters more for you let me know and see what we can do to clear it up.