Don't worry about trying to play them at the end of the last audio clip--that would never work and would sound bad. Instead, export each measure or whatever you're using individually but don't cut off the decay at the end of the audio.
ahh yes, like in RMX or REX beat slices and let them overlap. Very cool idea.. so you just have to do the math to figure out the timing of when to trigger them... (song_bpm / 60) * 4 (beats per measure). And if you are syncing them with a "master track" like you mentioned previously you'd figure out multiples of Audio.PlaybackTime("master").
if you cut up music into small enough sections (not too small) then you'd probably never have to re-sync right? Since the timer would keep everything together and the music wouldn't be technically "looping" because you'd be doing that manually...