Changing ‘#layer 1’ to ‘!#layer 1’ in the SpecDef file is necessary but not sufficient to obtain 3D output files from combine. The other requirement is for all input files to be 3D files and for the number of layers to match across all input files.
Changing ‘#layer 1’ to ‘!#layer 1’ merely instructs combine to use all layers from the input files (more precisely from the first input file which is used to define the grid structure of the output file, which is why it is important in this case for the number of layers to match across all input files), but if the input files only have 1 layer (as is the case for the example you posted, with DRYDEP, WETDEP1, and METCRO2D defined as inputs), the output will only have 1 layer, too.
As noted in the older thread in which you posted a related question, if you want to create a 3D file with concentrations (deposition is by definition a 2D variable, so there is no sense in trying to create a 3D deposition file, at least not using the traditional cartesian definition of 3D), you’ll need to update the run script to only define 3D files as input (i.e. CONC and METCRO3D, assuming your CONC files were created as 3D files with the number of layers matching METCRO3D, and potentially PMDIAG if you wrote it out as 3D file and the layers match, too) and also update the SpecDef file to only reference variables from these input files.