Hello,
You don't have to run 3dDeconvolve 64 times. The stim_times_IM option in 3dDeconvolve will generate one regressor per trial (i.e. single trial). Check the design matrix with 1dplot or look at the X.jpg image (note you have written X..jpg with two dots). Then, 3dLSS will estimate the betas for each single trial via Ridge Regression as recommended in Mumford's paper instead of the standard Ordinary Least Squares
Btw, I think your 3dDeconvolve should indicate -num_stimts 2 since you are only including one type of stimuli.
Hope this helps,
Cesar