The layout isn't consistant in the cartoon (heck, what is?) but I had done this type of research before. I no longer have any of my notes however. I had originally wanted to create the Ark and Quintesson Judgement Chamber as maps for Quake 3. Annoyances with the level editor led me to quit the project and they were never finished.
The main problem is that the ship's layout when it is in the air vs crashed is different. Also things move around during the course of the show. Some of the design was changed after the MTMTE pilot. For example, it is suddenly there is that building outside. It isn't clear what is in that building. Sometimes you can say the repair bay like you say, but other times a guy will walk in through the mountain entrance and make a turn and be in that room.
If you really think about how the layout is, you can make the argument that their base isn't actually IN the Ark, but below it instead. If you think about this, Teletraan-I is primarily shown as being on the right side of the TV screen. Then directly behind it is a rock wall that separates that area with the cavern where the dinosaur bones are. This would imply that a portion of the Ark's bottom hull had collapsed that it is possible that Teletraan is not in its original location. This is due to we know the bottom of the Ark lines up with the bottom of the thrusters, however the ship is stuck in the mountain at an angle. So if they enter at ground level (below the thrusters) it either means the ship is no longer intact OR there is a ramp/stairway or elevator that takes them into the ship where Teletraan is. But if there was a ramp into the ship, it would not explain why there is a portion of the ship with a rock wall visible in which to find dinosaurs. You will notice that after the Dinobots are put back in that room, they are buried in. But later someone had removed the rocks and put a door in there instead.
Because it is not consistant, you will have to make decisions on your own to figure out a proper way to render the base as a real physical object or environment.