It has been estimated that 80% of the guitars sold during this time were made in Japan.
When the Corona plant was started up, only the Vintage Reissue Stratocaster models were first produced (between late 1985 through 1986).
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.
Mid–1997 the CIJ logo was the only one used on Fender guitars coming out of Japan (with exception the Squire series).
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.
The JV and SQ guitars, as well as some of the E series, had USA parts (mostly pickups, switches, and potentiometers) that were shipped over to Japan to help speed up production while the new USA plant was being set up in Corona, California.
I really don’t know, but the MIJ logo Fenders were for the USA market.