@Wildstar - thanks for the suggestions and references. That would be a bummer that there is a scene in "Mirror, Mirror" that has them climbing up to the EMM
But, it isn't a total loss as Mytran's suggestion could work where that corridor to the EMM ladder entrance could be the deck below
As far as reconciling the layout, I'm taking the approach that the engine room is getting altered from short refits and/or Scotty's constant tinkering with his engine room. It's kinda like the constant bridge and engine room changing between the first 6 movies
Eventually I'll post up a progression of changes that room went underwent over the 3 seasons.
I think once I'm done with the engine room, I'll fix up my shuttlebay complex and then see where to put the engine room. Lotsa small steps