and both were being made at the same time from 1994 till 1997.This means that the the serial numbers starting in 1994 ran consecutively on both the MIJ and the CIJ models while the MIJ logo was being phased out.

Serial numbers have been used in various locations on Fender instruments through the years.
So, you can't afford that '54 Strat, or that '64, or even that '74 for that matter.
Some dealers simply go by the serial number, which you will discover can be far from accurate.
Some might go by the pot codes, but those could have been stock a year or more old by the time they were put into the newly finished guitar.
Mid–1997 the CIJ logo was the only one used on Fender guitars coming out of Japan (with exception the Squire series). I really don’t know, but the MIJ logo Fenders were for the USA market.
USA Fender wanted to stop the import of these guitars to the USA due to firing up their Mexican plant and due to the “too good” quality Japan was creating which competed with the USA models.
Most notably, production dates have been penciled or stamped on the butt end of the heel of the neck of most guitars and basses, although there were periods when this was not consistently done (1973 to 1981, for example) or simply omitted.
instrument production history, production dates have been applied to various components.
Regarding quailty, I have owned many of both these Japanese guitars and it is a fallacy that the than the Mexican made guitars and rival many of the USA models.