Well, this:
Indicates that even in the scale you are dealing with, you have miscounted somewhere.
Everything is on a grid, so generally you can just find something else to line something up:
Just remember if you are dealing with the bottom or the top of a wall when you are placing a block. I think you placed based on the top in some cases and the bottom in others.
You probably want to pick a fixed scale and go from there. I'm not sure what scale will work but I'm guessing 2:1... so use 2 Mythruna block dimensions for every muddy rogue tile. I think that even works out for the tables and chairs. The doorways will be two wide but then you can use half block borders to make the hole smaller for a door. (Eventually those will be solid blocks with a door overlay so it will be basically the same.)