I disagree that the deck plans should be considered totally canon, and I think that what is seen on-screen should be. For one thing, none of the deck plans of the refit Enterprise that are floating around on the internet have ever been seen on-screen (unlike the plans for the Enterprise D or E, which are prominintly featured on various displays). They are simply suppositions made for fun. And yes, I'm aware that this is too (and I think its a hell of a job) but I don't see how you can get around the fact that there is a corridor that leads out of the engine room, which if the room is where you say it is, simply cannot exist. It has to be further back.
The guy in the bay does give a good idea of scale - thanks. I still feel that there has to be only one bay, though, and that as suggested the launch track splits into 2 tubes at the end. If you look at the end of the inspection in Trek 2, and the funeral scene, there is actually a fair amount of space in there - it doesn't seem particularly cramped.
Still - its all for fun and ultimately as you say there probably isn't a perfect solution. The one I would personally go with would be something like the one below, which someone else has already suggested. This way you fit engineering in nicely, the corridor matches and you free up space in the torpedo bay. The only slight issue, as far as I can see, would be that the bottom of the intermix chamber sits over the arboretum. However who says there actually is an arboretum there? We've never seen it and the windows glow blue. Wouldn't they be green? And isn't it slightly odd to have a garden deep in the engineering section of a ship where space is at a premium?