The problem you're having is Dimon wasn't really made to handle Siemens DICOM files. Siemens will very often, but not always, use a mosaic format allowing for all slices of the volume to be stored in a single DICOM file. The Dimon program will take care of the numbering sequence usually, but won't compute the correct number of slices. The to3d program, on the other hand, is aware of the Siemens mosaic format and will find the multiple slices in each file. The GUI for to3d will show the multiple slices.

The changes you've done look roughly right; you'll have to check that the slice timing is correct. Without Dimon to sort the files, you'll also have to verify the file names are already sorted correctly, perhaps writing a script to expand the number of digits in the file names.