"You have no choice when there is conflicting evidence. We have to choose what parts we retain as "pure," what parts we reject entirely..."
Quite so. My argument simply concerned which parts were rejected entirely and whether or not we can legitimately reject on-screen canon. Opinion will, it seems, remain divided. And a war room will not be necessary. Just wear your Gorn costume and meet me at Vasquez Rocks
Saquist - Canon should not be "meaningless" in a project such as this, and I think CTM would acknowledge this. It is one of the primary sources drawn upon, in concert with the design intent (although my stance is still that intent need not be so slavishly adhered to).
Also, I'm not sure that your description of the intermix operation on the refit Enterprise is entirely accurate. On the Enterprise D, it is the case that deuterium and anti-deuterium (I think?) are injected at opposite ends of the chamber and regulated by the central dilithium crystal, from which the plasma stream emanates. But the refit chamber doesn't follow this method. There are two shafts, and no central crystal to regulate the reaction. Indeed, the actual crystal appears to be located in a seperate room, well away from the shafts - the reactor room where Spock dies. Evidence that this may be a crystal chamber can also be found in Voyage Home when Scotty peers at an identical chamber on the Bird of Prey and comments that the crystals are burned out.
Another theory I've read which may explain the workings of the refit shafts is that the shafts themselves are uniformly coated or treated in some way with dilithium, so that the matter & antimatter is simultanously released into the shafts where it is instantly converted into plasma energy. Further evidence for this is suggested by the simple "branching" of the horizontal shaft to the pylons. And now that I think about it, I wonder why a horizontal shaft is required at all? Couldn't the vertical shaft perform this function and have power conduits leading towards the pylons rather than an entire shaft?