@ don1reed:
I have only just started trying to use SH3 in any sort of real navigation way. I also came across this problem. I considered plotting my position 'by eye' from another map, or using the KM grid converter backwards by trial and error. This was the main reason for me downloading these mod files.
What I found was that those black/white marks on my map seem to correspond to the scale bar in the bottom left corner and remain a constant physical size when the map zoom changes. They do not seem to correspond to the lat/long marks contained within these mod files.
I realise that you have been operating this way with success for some time - indeed it was your posting
here that provided the inspiration for me to try it myself and would be interested to know how you plot you lat/long position onto the SH3 map.
Thanks
Didd