I'm learning to play Cephalic Carnage's 'Endless Cycle of Violence.' I can play all of it and I've got that down, but I'm having trouble seamlessly transitioning between certain parts.

The main recurring theme of the song is an eerie tap section down on the 1st string, that is directly followed by some stuff down the 6th string. Can someone suggest an exercise to help me move between these parts effortlessly? There's no gap in between the two, the transition is immediate.
As with every thing on guitar, practice the hard part until you are capable of playing it cleanly at full speed. To do this, take it down to a manageable tempo, and use a metronome. It is imperative that this tempo be slow enough to allow you to play it perfectly, with perfect technique. Slow increase the metronome to higher tempi. Do not increase the tempo until you are able to play it perfectly at the previous one. Continue doing this until you achieve the desired speed.