Hi! I wouldnt remove the 2nd throttle plates. I have looked at a couple tunes created on a dyno and the 2nd throttles are used at very high rpm. They are 100% open at low rpm (you can check using tuneecu, or tuneboy). Also if you change the 2nd throttle, you are gonna need to adjust the tune accordingly. You cant just open them and expect its gonna work right. Also, if your future has the bike on a dyno, removing them also eliminates the ability to use them for tuning.
Regarding the cats, there is one in each can. Maybe a set of TORS? They dont have the cats in them.