Unless you're acquiring really fast volumes (less than few hundred msec or so), the slice timing correction will make physiologic noise in your data unrecoverable by any means.  The slice time correction resamples the data acquired at X msec after the start of the volume and assumes that everything is Nyquist-sampled (ie. no freq higher than 1/(2*TR) Hz).  Any frequency lower than the Nyquist is correctly resampled as if it occurred at the start of the volume.  However, any frequency in the data that is higher than the Nyquist gets smeared all over the Fourier spectrum randomly depending on where it happened to bin.  Most (possibly anything slower than 200-400msec TR, due to higher harmonics of cardiac) acquisitions do not have a volumetric sample rate fast enough to capture physiologic noise.  If you do a regression-removal correction (stage 4+5 of PESTICA script), then in theory this noise will have been removed, and you can then do slice-time correction after PESTICA.  You mention combining moco and slice time, if your motion is pretty low level, then you could do motion correction after PESTICA (see Jones TB, Bandettini PA & Birn RM (2008) Integration of motion correction and physiological noise regression in fMRI. Neuroimage 42:582-590.).

For the slice timing order, if you specify siemens_alt_asc, then it detects whether you've got an even or odd number of slices and correctly follows the Siemens slice timing.  It ignores the AFNI timing header, as these are rarely populated correctly.  So if you're using the default siemens ep2d sequence with interleaved ascending, just use the default siemens_alt_asc and it will use the correct slice timing.  In AFNI, if you're using slice timing correction later, however, then you will need to use the appropriate alt+z or alt+z2 otherwise slice timing will be incorrect.  PESTICA should be copying all the header information, but I've not tested this specifically.  Does it work for you?
Erik