I was trying to build MK4 armor, which requires two of the MK3's. The problem is that the MK3 Power Armor doesn't stack which makes it impossible to put the two MK3 armors into the assembling machine.
I just ran in to the same problem myself! Sorry that was sloppy testing on my part. I have updated the mod to change the recipe to only require one MK3/MK4 armor for MK4/MK5.
