I think the small tube you are referring to is possibly the accumulator. This unit is used to smooth out any pulses apparent in the lines due to the nature of the pump. I have not used a kit without an accumulator so Richard will have let you know the effects of removing it from the system. My guess would be it may change slightly between each application due to flow rates etc. but Richard is the authority on the subject.

As for programming, there are general guidelines one can follow but your best bet is to contact other users of the system with similar vehicles/applications to yourself and inquire as to settings/tuners that have been used. Maybe we can have some feedback on this forum for you one of the other sections if you post a few questions there.