However, when I use manual size (wfactor, hfactor above) Matlab adds a white margin to the document at the left and right side. I would like to remove those margins because I need the plots to align with the text in the documents.
I tried editing the BoundingBox parameters in the EPS file before converting them to PDF. This works. But it is manual trial-and-error work and not very practical (especially because the plots are being updated all the time and there's a LOT of them).