I've created a Nyquist plug-in that makes it easier to make new CUSTMGUI raw files. Basically it just outputs a LABEL track in Audacity that has all the beginnings of each sample marked. You can just click on the label, then PASTE the sample and it will be in the correct spot.

You can download it here:
https://sites.google.com/site/slowmassacrelabz/dir-dev/dir-nyq/dir-hhb/hhbm