Success! I have fixed the keyboard problems, entering level codes and saving games works without any problems now. Somewhat tricky to do but it was fun.
I also changed the approach to crack the game for a bit of extra fun, whatever checksums there might be, they will not matter anymore!
It will also make it much easier to support any other versions of the game since my crack just consists of 2 tiny modifications. I'll have to add my changes to JOTD's source, expect updated version of the Settlers patch in the next days.