Well then it sounds like the problems were all with the ride vehicles and not the "stationary" parts of the ride - or were there troubles with the scenes and the animatronics? Really what was so expensive after the initial investment? Also wonder if they use the same ride vehicles now how is that any more reliable? Perhaps they needed vehicles from another manufacturer - dare I name them - ETF ride systems?
The ride vehicles used today are the same vehicles from 1982, just with a different paintjob. (I think the little "accordion protector flaps" between each car are an addition, though)
One of the big problems with the turntable was the fact that it had walls separating each showscene, not only on the "stage" where the blimps were, but also separating one train from the next. So this required a hanging wall "sweeping" along the track in front of and behind each train.
If it were simply a matter of a train running at the same speed as the blimp, it'd be far less of an issue. But when you add in rotating walls that are within the spatial "envelope" of where the ride vehicles operate, you can see why safety was a big concern. If the train sped up too soon or slowed down too late when entering/leaving the turntable, you'd have the train ramming the moving wall.
This is one of those concepts/designs where it can be difficult to grab just how complex it was without a moving diagram or model to illustrate...
A thought/armchair Imagineering moment: I wonder if a better/safer/easier design would've had the track-area wall separate from the turntable... Have it be a stand-alone piece that was supported by a track of some kind located between the turntable and the ride track. It would have no motorization at all, except perhaps between the exit and entrance of the turntable. Each wall segment would sit at the entrance to the turntable scene waiting for a train to come along. As the train entered the turntable, the rear car would somehow automatically "grab" the wall segment and pull it along with it. This would then act as the trailing "blinder" for that train, and also the leading "blinder" for the train behind it. Then, as the train left the turntable, the wall would disconnect from the back of the train, and be pushed around the curve to await pickup by another train.
Since the walls themselves would rely on the ride track motors for movement, there wouldn't be any danger of a train crashing into the wall if the turntable and trains became out-of-sync, but as long as train speed was synched properly, the moving wall would match up with the turntable's wall and all would be fine.
EDIT: Oh, and for Mickey2008, if you're looking for a history and ride-through of the original JII attraction, Martin's video can't be beat:
http://www.vimeo.com/3015806
-Rob