Dear Elijah,
If I'm right, there are two options to accelerate FS execution:
1) The first option is using the FS openmp implementation http://surfer.nmr.mgh.harvard.edu/fswiki/OpenMP. I haven't tested this way but openmp allows to open multiple processing threads, and it is supported for the most time consuming steps of FS.
2) The second is using the GPU capabilities. This needs to have access to a GPU card, and add -use-gpu flag in your recon-all call. This activates the execution of the gpus implementations for CA Reg, SkullLTA, Inflation1 and so on, reducing the execution time (in my expertise, to 4-5 hours per subject).
I recently developed a scheduler to optimize the FS workflow execution using the GPUs implementation and a left and right hemisphere steps in parallel. This will be published soon on the Springer NeuroInformatics journal.
I hope that this will help a bit...
Cheers,
/Jordi