The MIJ line is a little difficult to work out. Not only do they have top, bottom, and middle level instruments, they also have lines that are export and non-export. Generally speaking - their bottom of the line basses are basswood, the better ones are alder and top of the range have "American Vintage" pickups.... which is marketing speak for god knows what.
There are some rules of thumb when shopping for used MIJ - the larger plated tuners are the usually the alder instruments, smaller ones (similar to that of the HWY 1) are basswood..... but there are exceptions to this, particularly in the 90s.
Fender was pretty much blown away by copies coming out of Japan in the late 70's and in 80/81 contracted FugiGen to start putting Fender stickers on what were previously Fernandes/Tokai/etc... Early 80's Fender in the US was a strange time. They were making outstanding reissues of their 60's instruments (Fullerton RI's), but the 'Standard' line was an excercise in cost cutting - quality nowhere near what was coming out of the Japanese factories... (IMO)
IMO a great way to judge the quality of a bass is by looking at the at the maple woodgrain in the neck. The higher graded wood reflects on the standards employed by the company at the time of manufacture. Good quality maple has a fine grain texture to it that sometimes goes flame or birdseye. Have a close look at a Musicman neck compared to a Fender MIM and you'll see what I mean. 80's MIJ instruments are sought after but IMO early 90's basses seem even better.