Not to take anything from this, because it looks great and its taken alot of work, but it isn't right. This is more the fault of the designers in Treks 1 & 2 than you though. Specifically, your torpedo bays are waaayy too small. If you look at Trek 2, that one bay is bigger than what you have here, and if we accept that there are in fact 2 bays, then it creates more problems. Look at the width of the exterior structure of the entire torpedo bay and compare it to the bridge, and the landing bay, to get an idea of how much space is in there (ie, not much at all). Now, if there are 2 bays and the other bay is equal to the size of the one seen on screen, then they just don't fit into the structure (and there's certainly not enough room to get a funeral party in there). Also note that in the funeral scene there is another level above Kirk & party. Logically that level is part of the neck, and not the torpedo bay, as the bay isn't big enough to have 2 decks (look at the airlock size). Therefore if there are 2 bays then it makes no sense for there to be a seperate level above one of them. The only thing that makes an argument for there being 2 bays is the fact that it is trashed in WOK but looks undamaged later (perhaps damage control were just really efficient that day?)
Also, I think we have to accept that main engineering is further back in the secondary hull. Why? Because of that corridor we see in TMP and the first attack in WOK. There's no 2 ways about it: if engineering is where Shane Johnson and Mr Probert say it is, then that corridor extends into the deflector dish. It has to be further back for it to fit.
The torpedo bay in WOK looks pretty cool, but they dropped a major bollock on the design side. For one thing, there's nowhere for the intermix chamber, unless we accept that its between the torp tube arms. I think Shane Johnson came up with that solution because its the only one he could think of that allowed his layout to follow Mr Probert's design drawing, but it is ultimately pretty silly. Also, note that at the end of the inspection scene, alot of trainees disappear off to the rear of the bay - to engineering, perhaps? - which would strengthen the more logical assumption that engineering is further back. And the entire layout of the bay is baffling. To load a torpedo, the arm must retrieve it from storage (wherever that is) and lower it on to a long track, where it then travels (pretty slowly from the on-screen evidence) down to the launch tube. I'd estimate there's a minimum 30-second loading time for each torpedo because of this design - plenty of time for some nasty Klingon to pound your ship while you arse around loading your gun. Why not use the bay itself for torpedo storage so that they go straight into the launch tubes when needed?
As you are finding, I think the design problem with this Enterprise (and don't get me wrong - its the best looking of all of them) is that its just too small. The landing bay, and the shuttlepod docking at the airlocks in Treks 1 & 2, give a good sense of scale and size, but the interior set design of main engineering and the torpedo bay (or bays) bugger things up because they are not logically scaled. And there's a big corridor.