1.TRD intake will not fit with the phantom supercharger because the airbox housing extends to where the compressor will be and the opening is facing the throttlebody. Best bet here is to sell the TRD intake to someone else and just get the TRD/HKS/K&N filter if you are looking for a high quality filter. Exhaust is not required but you will get better results with it....not a huge gain like you will with a 300-400 hp turbo remember though.
2. TQ dip is obliterated. You will have huge torque gains down low and about 30 to 40 hp+ above 6000rpm. If you go with e85 those gains will be better. If you go with the 1.5 dump conversion you will get more top end as well(adds extra batteries to the array).
Most people are going from 173hp stock to about 205hp with the standard kit and 215hp with the 1.5dump addition.
3.BPB has been tested with the kit by @
Shiv@Openflash and there was no appreciable gain when using with forced induction. The effects of the BPB is negated by the addition of a pressurized manifold from the supercharger.
Hope this helps!