Here's my Jag I just mutated...Warmoth Strat baritone neck - meant I had to move the bridge back towards the tailpiece to get the corresponding 14.25 inches from the neck's nut to 12th fret. Strung with baritone XL157's and tuned BEADF#B it has freaked out everyone who's heard it..the SD Antiquity II p/ups and PIO cap and 250K CTS pots add to the overall vintage grunt...I did it as an interim as I am in the middle of a Fender Bass VI build (USACG neck and body, more SD Antiquities) - you would have to check if you had enough body space on yer JM to get 15 inches from tailpiece to 12th fret, as a Bass VI is 30" scale...
The Bass VI body had to be extensively modded to make way for the Jag pickups...USACG cut their Bass VI bodies from a 1962 Bass VI template which has Strat pickups and a 3 way switch...all Bass VI's from 63 to 75 were Jag pickups and a 4 way switch...and if you want to do it totally Fenderstyle you gotta trim the headstock too, as USACG have a slightly different head profile so they don't have to pay license fees to the Big F...
Is your Jagmaster shortscale? I just took the neck and body down from where they have been drying, and the Bass VI has a distance of 4.25 inches from the centreline of the bridge to the tailpiece where the stringballs fit. The distance from the centreline of the bridge to the heel of the neck(neckpocket beginning is 8,5 inches...that should be all the measurements yo need. The Warmoth bari neck and the USACG neck should both fit straight into jour JM bod..it just depends on whether you have the length in the body to fit the Bass VI dimensions , as I have also just checked my Jag mutant bod against the Bass VI, and the Bass VI bod is a good inch and a half longer(from neck pocket to bottom strap buton. Personally, the Warmoth bari neck might be the better option, unless you really want a shortscale 6 string bass, as you can play massive 6 string chords on the baritone without struggling or freaking out your amp, but on a Bass VI that is not possible with the Bass VI 25 to 95 string gauge...
I will be stringing the Bass VI in baritone gauge just like the Jag bari conversion so I can still get fat chords...