Fusion LTK has a tool specifically for what you are trying to do. Its name is ClipData.
You'll need two switches (variations of the command line) to accomplish the task. The first switch is the biaselev:# (bias elevation of number equal to #). From Fusion's manual:
biaselev:# Add an elevation offset to every LIDAR point: # can be + or -.
So, let's say the minimum z value is 702, then, you would have /biaselev:702 to subtract all z coordinates with 702.
The second switch, which offsets x and y, is the nooffset. See its description from the manual:
nooffset: Produce an output point file that no longer has the correct georeferencing. This is used when you need to work with the point cloud but cannot reveal the actual location of the features represented in the point cloud. This option modifies the header values in the LAS header for the output files.
The complete command line for your case would be written like the following:
/ClipData /biaselev:# /nooffset InputSpecifier SampleFile [MinX MinY MaxX MaxY]
where InputSpecifier is the gross lidar cloud (.las file), the SampleFile is the new .las file with the offsets and [MinX MinY MaxX MaxY] are the minimums and maximums x and y from the gross lidar cloud, respectively.
Here I wrote a detailed answer which teaches how to use ClipData that you can adapt for your case using information from this post.
Just to exemplify that this works, I ran a test with one file of mine. Here is a screenshot of the new .las file's header.
The "LAStools" toolboxes in ArcGIS, QGIS, and ERDAS IMAGINE all operate on one LAS / LAZ file at a time. The "LAStools Production" toolboxes in ArcGIS and QGIS take folders and wildcards instead of filenames as input and can then be run across hundreds of tiles and on multiple cores.
For faster performance it is instrumental that you first run lasindex to create *.lax files for each tile. Unfortunately the internal structure of ESRI's near-identical *.lasx files is a trade secret so you will have to index twice. Kind of a shame as these proprietary *.lasx files seem to be only a minor variation of the open source *.lax files LASindex produces.
Best Answer
I also added -labels to the command line options and that seems to have populated the grid with everything i need, despite having the "Produce Labels" checkbox checked.