Also, another thought (that you may have already considered and dismissed?) is to make the "emergency manual monitor" room a seperate "balcony" type thing? running along the upper side of FJ's "energy converter" room. This way, those energy converter things (which probably put out a lot of light/heat/noise?) remain seperated off into their own dedicated areas?
P.S. If you look closely at FJ's cross section (with a magnifying glass) you can see that he apparently elevated the main floor of engineering by about a half a foot or so? It requires a "step up" from the entry foyer, but that might help with your headaches?
Anywho, great work, I'm looking forward to more of the same!