Looking at this, it would APPEAR that you're taking some of the set diagrams (from the stage layouts) and using those to place them into the ship interior. Is that correct?
Also... it would appear that you're using the "versus the carrier" diagram as the scaling reference instead of EITHER of the two most accepted lengths (947 or 1080 feet). It's intriguing to note that, give what you've shown so far, the bridge and the bridge turbolift DO seem to fit into the model without any of the "gymnastics" folks around here sometimes go through. SO... what's the length you're working from as of now?