Q: Does anyone have a (Matlab) script or know of good software for applying a temporal filter (e.g. bandpass) to timecourse datasets?

A:Have you tried NIAK? It has high-pass and low-pass filtering options. You can find more information on it here: http://wiki.bic.mni.mcgill.ca/index.php/NiakFmriPreprocessing under the section: “Correction of slow time drifts”.