(1) I no longer recommend the use of the -fwhm or -fwhmxyz options. Instead, I recommend that you use 3dFWHMx -acf to get the mixed Gaussian+exponential model fit parameters (a,b,c) from your subject level residuals, take the mean of those across subjects, and use those as input to 3dClustSim with the -acf option. If you are using an up-to-date version of afni_proc.py for your individual subject analyses, then it will give you the acf parameters now.
(2) You do not halve the p-values. The 1-sided and 2-sided testing inside 3dClustSim now does that for you, and gives you the tables for each case of sided-ness and NN connectivity-ness. You probably should just use the -LOTS option (along with the -prefix option) to get the values you want in nicely formatted files.
(3) This stuff is the subject of a paper we are submitting very soon (hopefully, Friday). When we can post a link to it, it will go here, never fear.
