optimizing a bash script chain - speed suggestions?
It's not related, but please don't mind if I use an "answer" to just comment : it seems I can't comment, maybe because I don't have enough points yet to do so... 

Tarrasch, if you still use csh for your shell, please do not script in it.

Please read: http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/

Use instead sh, bash (or even ksh). And better to stick to sh-only because that's what's all unix system rely on (and rc scripts, for example, are based on).