It works with the same steps/mm and jumper configuration of the original drivers (417.5, just third pair). Tested all axes as well. All good.
Z axis has all jumpers in, and set for 3200 steps/mm, so it appears that the jumper configuration is the same for the V2 of my drivers as for the original ones, after all. At least for 1/16 and 1/32 config.
I can definitely use the single hotend firmware while you troubleshoot the 2 in 1 firmware, since I never even used the second extruder until now.
The big question is: could this have been the reason for the layer shifts?