Go to Tools > Data > Batch Editor and run the following command. It will modify all Pokemon in all boxes.
.OriginalTrainerName=PKHeX
.TrainerTID7=123456
.TrainerSID7=1234
.OriginalTrainerGender=1
.ConsoleRegion=0
.Country=1
.Region=2
.OriginalTrainerGender=1 sets the gender to female, use 0 for male
.ConsoleRegion=0 sets the console region to Japan (for other console regions use 0 - Japan, 1 - Americas, 2 - Europe, 4 - China, 5 - Korea, 6 - Taiwan)
.Country=1 sets the country to Japan, for other countries check this https://github.com/kwsch/PKHeX/blob/master/PKHeX.Core/Resources/text/locale3DS/countries.txt
.Region=2 sets the region to Tokyo, for other regions check this https://github.com/kwsch/PKHeX/blob/master/PKHeX.Core/Resources/text/locale3DS/subregions/sr_001.txt