I would suggest starting with the tune found in the "R3T Derestricting" thread that is just a search away. Be sure to hold on tight when you take the bike out for a ride. I would also suggest not riding it too much without the tune, since you have already changed the intake and exhaust.
Go to the resources tab up top and look for the Tune labeled blah blah blah Nels Touring tune or something along those lines. . He tweaked my 2013 R3T with RamAir and Tors to build that tune. It should work fine in yours. The key word you are looking for is Nels.