My lovely wife ordered my 2014 Roadster a new ramair for Christmas and I have been trying the search function for a couple days. I could not find a consensus answer on whether to remove secondary butterflies or not. My only mods are an opened up exhaust canister done by myself and the tune from claviger for a stock rocket.
Just use TuneECU to load a tune that has the secondaries open. I don't believe you will need to remove the butterflies that way and it will lessen the risk of dropping something into your motor, not saying you would, but zero chance is better than slim to none.