Mike,
Is the total price $1200 to you, with the 1/3 Acura amount. If it is this sounds like a pretty fair deal. I know the trans case cost alone is around $500.
In regard to the part being redesigned, that is not really the case(no pun intended!). The early transmissions had a manufacturing defect/quality control problem. The groove, in the transmission HOUSING, that the snap ring fits into was cut to wide and caused the countershaft assembly to slide back and forth too much, which kind of acted like a slap hammer and broke the snap ring. In 1993 the transmission case defect was eliminated, by resolving the production issue.
Please bear in mind that Acura really has no liability to contribute to this repair, the car has been out of warranty for 5-6 years. So enjoy the discount and get back in the driver's seat and have some fun.