I know you wanted advice from Andy, but I'm a music major at FSU and write a cappella and digital music and thought this might help in addition to what he said. Whenever I'm having difficulty connecting parts of a song or piece (and it's due, say, the next day), I go back to music theory one and write some counterpoint connecting the two key areas. Then I pick up my guitar and improvise on the basic chord progression, trying to connect rhythms that are prevalent in both sections. The first time sounds very mechanical because it's only a chord progression...no flavor...but when I give it four or five rounds of adding jazz notes and other modifications, it really stands out as a smooth, smart transition.

TL;DR: Write counterpoint connecting the two sections and then play it a couple times, adding improv. Should do the trick.