I have a MIJ Jag-stang from the second release Fender Japan produced in the early 2000s. I purchased mine new in 2003. Back then, the retail price was $500, and I bought it from a store in West LA that was (and probably still is) known for knocking sales prices way down from the retail price. So I probably paid about $400 and some change, plus tax.
Except for one detail, I'm fairly certain the the early-2000s reissue of the guitar was identical to the late-'90s original issue. I believe the electronics were the same. That one detail that was different was the back of the headstock. The one I have says "Created by Kurt Cobain" in type that was under the lacquer, whereas I think the ones from the late-'90s have an oval sticker on the outside of the lacquer that says the same thing. I always thought it was kind of tacky that it said that on my guitar, and I think it was a good decision that the back of the headstock on the new MIM Jag-stangs doesn't say anything about Kurt Cobain.
However, I wonder if the pickups on the new MIM reissue might be different. The MIJ versions had specific names for the pickups. I forget what the single-coil was called, but I seem to recall that it was modeled after a Strat single-coil, and the humbucker was called a "Tex-Mex Special," or something like that. I used to come to this same website back then. I remember that people here tended not to like the humbucker and very frequently replaced it. There was a specific Seymour Duncan humbucker that a lot of people on this website agreed was a good replacement, but I don't know any more details. I left my Jag-stang with the stock humbucker. You could probably find what that humbucker is somewhere on this site if you look, if you are interested in finding this out. There were also people who weren't crazy about the single-coil. But it wasn't an expensive guitar, so it was hard to be surprised that there were hater or people snooty about the quality of the guitar.
I haven't seen, heard, or played the new MIJ Jag-stangs, but I have read about them online. I was considering buying one online, but decided not to. The descriptions of online for the pickups are different than they way they used to read. No mention of a Strat-based single coil or a Tex-Mex anything. The Fender website says it is a vintage-style single coil and custom humbucker. This makes me wonder if they updated the pickups based on complaints about the electronics on the MIJ versions.
I must say, though, that I always liked my Jag-stang the way it was. I thought it was a good guitar. I haven't played it in almost a decade. It currently resides in the large basement of my father's house, in a different state, where I have a bunch of old stuff stored. I haven't had a chance or reason to relocate all that old stuff of mine stored there.
But I recall always liking the guitar. I will say, though, that I agree the humbucker isn't of the highest quality. When I would play with the humbucker alone, it did sound kind of ####ty. I thought about replacing it with that Seymour-Duncan humbucker or another one I was considering at one point, but I never did. I thought that when the two pickups were both turned on, the combination sounded good to me. And I thought the single coil by itself had a great sound, but it was a little weak on its own. But that is certainly also true of the neck pickups on all the Mustangs that I have played. Then again, you can get some pretty good Tele-type sounds out of the neck pickups on Mustangs. Maybe the same is true with my old Jag-stang. I'd have to play it again to know, but that requires me to travel to where my father lives, and to find a good amp.
Furthermore, about a year-and-a-half ago, I was at a Guitar Center, and I asked the question: What is the difference between MIM Fenders and MIJ Fenders. I was told, Japan is know for its superior craftsmanship, Mexico is known for having better electronics. This further leads me to believer that the MIM Jag-stang electronics may be different or improved.
After 2003, I went on to buy other, more expensive, fancier guitars, but I always considered my Jag-stang my main guitar until I left it with my dad in 2011, when I temporarily moved to Japan, ironically. But I mention that fact to say that if you're looking to buy a late-'90s or early-2000s Jag-stang, I personally recommend them and don't object to the stock pickups. But if you have the opportunity, it might be worth your time to compare the sound of the pickups between the two versions.
There is something worth mentioning that people don't seem to talk about too much when it comes to the Jag-stang. The neck is really skinny. Like, really skinny. Prior to purchasing my Jag-stang, I had taught myself to play guitar gradually over several years on an Epiphone SG. Perhaps because of that, I have found that, these days, my hand feels most comfortable on a neck with the thickness that Gibson and Epiphone guitars offer. So I'm surprised I didn't have more difficulty switching from my SG to the Jag-stang. The next year, in 2004, I bought an Epiphone Sheraton II, and I don't recall having a notable problem switching between the two.
But I still like playing Fender guitars. The reason I'm explaining all of this is to illustrate just how skinny and thin the neck on the Jag-stang is. One of the cool things about guitar stores in Japan is that they are chock full of very cool, sometimes very unusual Fender Japan guitars that you can't easily get in the States. When I first arrived in Japan, that was the year that Fender Japan was issuing a new slew of Kurt Cobain-based guitars. And the MIJ production of Mustangs was in full effect. There were all kinds of different Mustangs in every possible color. One of them was the "Kurt Cobain Mustang." I played a few of those at different stores and eventually bought one.
I initially thought the KC Mustang might be similar to my Jag-stang. Whereas normal Mustangs have two single-coil pickups, the KC Mustang has a neck single-coil and a bridge humbucker, like a Jag-stang. But that Japanese issue of that guitar also has fancy Seymour-Duncan-labeled pickups in both the neck and bridge pickup postions. They sound good.
**But more surprising to me was how thick the neck was. Yes, all Mustangs have a short scale of 24", but the neck is WAY thicker than on my Jag-stang. I was really surprised, because I had read that Kurt Cobain had selected his favority Mustang neck to be used as the basis of the neck for the Jag-stang. But on the Mustang matched to the specs of the guitar he used on the In Utero tour, the neck was much different than the Jag-stang neck. I like the thickness, personally. I think anyone would be challenged to find a Fender neck as skinny and thin as the one on a Jag-stang. I'm not an expert.
I continue to play, casually, to play some of the guitars I have acquired over the years. I keep that KC Mustang as part of my arsenal. I also play a Gibson SG, and a Firebird.
They are great guitars. I would recommend getting solid guitars that aren't based on the names of dead people.