Alright-now it's all coming together. So you're changing your air intake system from the stock air box to turn outs with essentially K&N's on it. And you have the JCW's on there now-so no change to exhaust. I see where you get the 157 from the calculator (assuming sea level).
In that case-you're original question was should I change the pilot jets and adjust the pilot screw? When I did mine it called for 160 mains-I put in 155's. Almost everybody that I talked to said you want to go with 45's for the pilot jet. And the general rule of thumb is when adjusting the pilot screw if you have to go more than three turns out you need a bigger pilot jet (in case you leave the 42 in there). I left my pilot screw at 2 turns out-haven't dynoed yet so no hard results-but she runs well.
Maybe one of you '04 guys can chime in-my understanding was if the pilot screw is plugged it's a standard screw driver not a D tool type. Triumph put that "fancy" screw on so we couldn't screw with the screw
