Hi, Robin-

Re. your Q2--
You can choose your desired "alpha" values in 3dClustSim with this option:

-athr a1 .. an = list of corrected (whole volume) alpha-values at which
                  the simulation will print out the cluster size
                  thresholds.  For each 'p' and 'a', the smallest cluster
                  size C(p,a) for which the probability of the 'p'-thresholded
                  image having a noise-only cluster of size C is less than 'a'
                  is the output (cf. the sample output, below)
                  [default = 0.10 0.05 0.02 0.01]

Re. your Q1--
You have cited the Big 3 of sources for clustering/thresholding stuff in AFNI to date. There has been a bit more work on ETAC by Bob, but the main point of it is included in his slides quite nicely.

Note that another REALLY relevant issue that a surprising number of published papers still do not get correct is that of what sidedness of testing to use. Using a pair of one-sided t-tests without correction doubles the FPR of reported results (and actually, does that while using a doubled p-value, which might even cause further FPR inflation). This is a model- and simulation-free result-- it is purely a mathematical point. As much as you strive to have a 'valid' p-value threshold, please also use correct testing for your hypotheses:
[www.ncbi.nlm.nih.gov] (HBM)
[www.biorxiv.org] (bioRxiv)

Re. your Q3--
Well, I'm not sure if there is a question there, or what the precise question is.

--pt