1. The RMM improves shifting and grip by keeping the transmission from twisting. All aftermarket RMM more or less do the same thing so I'd say leave it unless it's broken.
2. That is the clutch slave cylinder inside the transmission. The yellow cap is for reverse bleeding the brake fluid through it and into the reservoir(Which I highly recommend you grab some brake fluid and
one of these and do it! Changing your fluid could possibly prevent slave failure) The other line goes back to the brake fluid reservoir.
3. FSWerks short shift plate. It reduces the shift throw. No negatives there! Only reason you might change it is to go with Mountune Shift plate as it reduces even more than FSWerks, but not worth it unless you feel it's not enough. Even then I'd probably say grab a boomba short shift arm instead.