With fuel injection you have to buy a Screaming Eagle Race Tuner (SERT) or Power Commander or similar system (zippers, and S&S have their own). An ignition by itself won't do it since you need a way to control fuel levels as well.
I am assuming that you have had a "reflash" done to your ECM already or it would be running very lean and have caused damage already. With that reflash, your fuel and ignition have been compensated for the big bore. If it runs good enough for you and you're not having performance or overheating problems, you can just leave it alone. As long as you aren't pinging/detonating the timing is fine and if you need to add a bit of fuel you can buy a DFO or Vance and Hines Fuelpak to add fuel...these units are cheaper than the SERT or PC III.
If you really want the most from your build, take your bike to a well trained dyno tuner...like the ones certified here
http://www.mmgmanagement.com/ and let them do whatever they need to do; whether it be a SERT/PC III or some other route, they will get the most out of your build while maximizing fuel economy and ensuring you are not running lean or in a dangerous condition.
