sorry to chime in so late on this thread but i can help out a lot on this case, as i own all three of them, displayed below
I have a white MIM Jimmie Vaughan 2001 Custom, a Black MIJ Blackie Replica Custom, and a Red 2005 MIA Usa Deluxe.
Let me start with the MIM,
In stock form the MIM was a nice OK guitar. The hardware was absolultely great and the JV neck is better than my soft V neck on my USA (more confortable) The bridge is a fender vintage bridge, and the tuners are Fender Vintage, this guitar actually has the same hardware as fender customshop guitars.
The pickups were ok, but quite ordinary, in std form they were Fender Tex-Mex, I replaced them for a set of USA standard pickups, they were slightly better but still only ok. I have now replaved them with dimarzios and lost all the hum, but also lost some of the fender magic, ill be going back to a set of lace holy grails for that guitar i think.
Standard MIM pickups hum like mad. almost pointless in a high gain situation.
The body is good and the neck is also good, im actually really happy with this JV guitar, but out of my 3, its the worst one.
My MIA 2005 USA Deluxe is flawless in every way, every detail has been perfectly finished and assebled, the pickups (SCN Noiseless) as perfect and the S1 switching is amazing, the guitar is a jem and i love it very much, BUT because its so new and flawless im affraid to play it, in all honestly ive had this guitar for about 9 months now and ive played it for a max of about 2 hours all up. i just cant bring myself to play it in fear of damaging it. The MIA deluxe is night and day to the JV its the difference between a nice looking girl, and a hot girl with great boobs, shaven areas, flat tummy and perfect face face, really its that good.
now here is where it gets interesting. I bought a MIJ blackie off the bay a while back for fun, actually bought it just to steal the pickups out of, the guitar sold for $300,i was gonna put the pickups in teh white strat.
When it arrived i plugged it in and the Angels sang in perfect harmony. this guitar is most definatly in the same league as my MIA, pefectly finished, awesome japanese hardware (gotoh) and it sounded like heaven, the wood is also lighter than my JV and about the same as the MIA. This guitar has some dings but its sooooo cool. This guitar has a C profile neck and is the most comfortable guitar ive ever played, it sounds perfect, the frets are nicely finished and all the hardware just works, the trem is great and electronics are great too.
I personally have more fun with my MIJ than any of my guitars, it can pack a deadly distorted punch and provide some of the sweetest cleans youd ever hear, the MIJ is a great guitar and should not ever be over looked, its so miles ahead of the MIM and as someone else said, most probably on par with the MIA.
I love my strats