I don't have your example so I had to use one of the JMP sample data tables. Replace those lines for the initial data table with your own.
Names Default to Here( 1 );
// use sample data to illustrate
dt = Open( "$SAMPLE_DATA/Fitness.jmp" );
// delete non-numeric data columns
dt << Delete Columns( { :Name, :Sex } );
// make empty container
table = Associative Array();
// get each data column and create (key, value) pair (key = col name, value = 8x12 matrix)
For( c = 1, c <= N Col( dt ), c++,
data = Column( dt, c ) << Get As Matrix;
If( N Row( data ) < 96,
data |/= J( 96 - N Row( data ), 1, 0 );
);
table[Column( dt, c ) << Get Name] = Transpose( Shape( data, 12, 8 ) );
);
Close( dt, No Save );
dir = Get Default Directory();
content = table << Get Contents;
For( t = 1, t <= N Items( content ), t++,
dt = As Table( content[t][2] );
file path = dir || content[t][1] || ".CSV";
dt << Save( file path );
Close( dt, No Save );
text = Load Text File( file path );
eol = Contains( text, "\!n" );
text = Munger( text, 1, eol - 1, content[t][1] );
Save Text File( file path, text );
);