Nick,
just a short answer, before Christoph can get back to this discussion.
You can trim the ends of your custom loop by cutting it. I'd look at the loop in the track editor, so you can see the wave form and can tell where the silence starts. Adjust the slider, so you see the waveform enlarged and can trim exactly. To cut the loop, use the keyboard shortcut "⌘T" after postioning the cross hair.
Only, I do not see, how cutting off the silence will help. You will want to cut exactly at the boundaries between measures, for your loops to stay in sync with the beat of the music.
It might be preferrable to drag the waveform to extend the sound into the silent region with the flextime editing tools. If you enable "Follow Tempo and Pitch", you can drag the blobs in the waveform to make the sustain longer.