if it helps, Godot, during one of his more beneficent phases, once designed an across-session analysis for us. registering data across sessions (i.e. days) involved the following steps:

1) align anat2 to anat1 using 3dvolreg (using the -clipit -twopass, -twodup, -zpad, and -rotcom options)
2) create epi Tshift reference run using 3dTshift on epi1 (skip any first few timepoints that won't be used in the analysis, if you have any)
3) register and Tshift epi1 (within session), then concatenate epi1 runs
4) pad epi1 with 3dZeropad to allow for difference in scanning space between sessions
5) create epi2 Tshift reference
6) perform intra- & intersession registration on epi2 using anat2_registered2anat1 as -rotparent and epi1_Tshift.padded as -gridparent (use epi2_Tshiftref as -base, and also use -zpad, -clipit -tshift options)
7) concatenate runs for epi2 runs to epi1 runs
8) smooth
9) analyze

Godot - are you still a believer in this method?