Back in the same place as my EC, I measured my makeshift round mirror stop (photographer's right side), and it's roughly 8mm diameter but it's a little compressible. The focus scale distance, focus on the groundglass, and focus with a GG placed on the film rails all seem to be in agreement. It should be pretty clear how to get the GG in place. There is a metal frame on the upper side. The foam is on top of the GG pressing it down onto a hard stop, so the foam doesn't set the GG position, but if it rots the GG could become loose.
@itsdoable does that piece on photographer's left side really set the resting position of the mirrors? On mine it's covered in some crusty-looking foam. The lower mirror is a bit out of place, which is annoying but only an issue with certain lenses. It doesn't seem like the lower mirror should touch that stop?
@wakks what lens do you have? If you post pictures of the lens someone may be able to to tell if it's mis-assembled. Are you sure you're reading the correct distance scale? Most of the focus helicals have scales for 2 or 4 lenses, and the index mark for the distance is not at 12 o'clock but some place to the left, so I often have to double-check myself when trying to read a distance.