Also, the new -xsave option to 3dDeconvolve will save the X matrix, as well as the matrices [X-trans X]^(-1) and [X-trans X]^(-1)[X-trans] into a file. This file is normally binary, but if you set environment variable AFNI_XSAVE_TEXT to YES, then the file will be written in text mode. You should be able to figure out what is what in this file without too much trouble.
The -xsave code is only executed if you actually compute results (e.g., you can't use -nodata) AND also use the -bucket option to output results.